Josh Moore: kick that off.
Josh Moore: So yeah Good morning, so i'm just more.
Josh Moore: From the open microscopy environment.
Josh Moore: Thanks everyone for coming and we'll do a round of introductions in just a second tried to keep it under 20 Minutes that we're not.
Josh Moore: spinning too long on it um for anyone who's here for the first time, so to explain very briefly, this is generally a fairly technical conversation so you're welcome to kind of get into the details a bit.
Josh Moore: We do only have two hours um with the goal of having a standard file format that we're all using in microscopy.
Josh Moore: largely focused on this concept of n G F F, I mean f's did I say that I say enough so it's basically a cloud based file format that you can store in s3.
Josh Moore: Many of the things we'll talk about, though, are also applicable to hdfs and to tiff and so, in general, we want to come up with a generalized solution, a small number of formats, that we can all use together.
Josh Moore: And kind of in the madness that has developed over the past, you know 20 ish years, those are least the 20 that i've experienced and it goes back farther.
Josh Moore: Where we've needed something like bio formats to actually access our data so that's the goal.
Josh Moore: And the general focus of today will be trying to help.
Josh Moore: Others, ie more of you to get involved in this.
Josh Moore: Experience in this effort i'm add new specifications update the implementations in the various languages, the currently their.
Josh Moore: Java Python and javascript implementations can we as a Community start working together to make that happened a bit faster, so this is a snowball snowball process.
Josh Moore: um, I will start pointing at people i'll kind of go around my screen, I will warn in the chat who's up next for introducing themselves kick it off with Jason and then sets up that.
Jason Swedlow: morning quickly i'm just as fellow at the University of Dundee.
Jason Swedlow: And I work with josh and many of the others somewhere on the screen on the on the project.
Josh Moore: Still around he turned off his video he may have kids so.
Josh Moore: Go to Constantine then.
Constantin Pape: Yes, hi and Constantine i'm a postdoc with an occasional Heidelberg and I work on vacation for large electron microscopy data until of this process i'm also interested in developing the five five minutes to share this.
Deborah Schmidt: hi i'm Deborah i'm obese or something yeah and kind of having slept was also here.
Deborah Schmidt: i'm currently working on side view, where we are thinking this 3D virtual reality view or we might want to be present a project, for example in our that's at least one idea.
Deborah Schmidt: And so, by unprepared for this meeting, not exactly sure what will happen or what I can contribute but i'm looking at to listen and just get an idea of what's happening.
Draga Doncila Pop: hi i'm draga i'm done on the student in while I just finished on those in at one atmosphere and i'm currently contracting for an apartment and basically here today to talk about I guess collections dimensions and resolve.
Josh Moore: Oh yeah if you know the specification, you want to talk about do mention it excellent thanks trying.
Guillaume Gay: i'm in charge of kind of standing Romero on the lumina campus in masa and i'm interested in bizarre because I think I face a lot of different.
Guillaume Gay: Images a format and so on, so i'm happy to engage with the problem.
Eric Perlman: americ problem and i'm at the Jackson laboratory actually have two hats that I care about this one is, I still do some contracting with dobby Bach whose lab I was in.
Eric Perlman: For large scale em reconstructions which a bunch of you have here have actually worked on as well, but I also now at Jackson we have we use Romero, and so I care about how we can have.
Eric Perlman: Access to very large slide scans and things of that sort.
Josh Moore: Oh young years super quiet okay.
Josh Moore: Maybe someone else or fix this quickly okay cool.
Jean-Karim Heriche: Sorry, I forgot, I was muted.
Jean-Karim Heriche: i'm shonky I am I work at end I do computational support for the cell biology and biophysics unit, so I encounter images a lot.
Jean-Karim Heriche: In various forms and formats and i'm also work package leader in the ios LIFE project, so the European open science cloud.
Jean-Karim Heriche: Implementation targeting the life sciences and for this I also we present your by Beijing in that project, and so we are particularly interested in how to deal with images in the cloud and particular image data access.
Thanks Yun you want to try it again.
Josh Moore: Yes, thank you.
Jan Albrecht: Wonderful okay so i'm young i'm workouts.
Jan Albrecht: And we're heavily interested in having a standard across the image field, because we want to build.
Jan Albrecht: yeah methods to include all tools together and.
Jan Albrecht: To provide some.
Jan Albrecht: yeah layer to join all of them.
Jan Albrecht: makes sense.
Jon Fuller: hi i'm john fuller.
Jon Fuller: i'm a scientific software engineer and have some experience in cloud I protecting and work for a dossier a smallish pharmaceutical company and bustle.
Jon Fuller: also contribute to the orbit image analysis and open source software for whole site imaging.
Jon Fuller: And at dorsey we're interested in primarily household site images and specifically today, I was interested in how to exchange annotations along with the image themselves.
Jon Fuller: Thanks.
Juan Nunez-Iglesias: So i'm one i'm a researcher at monash University in Melbourne and I work on the Perry and second image mostly and I would like to talk about physical spacing and physical position in the spec.
Kyle Harrington: i'm kyle i'm a group leader at the Max kell brook Center in Berlin we're particularly interested so i'm also representing the helmholtz imaging platform so we're kind of a consortium of all the Humboldt instance in Germany.
Kyle Harrington: We work on a bunch of scales, but here we're particularly interested in storing the storage of mesh formats, I was involved in that forum discussion a bit.
Kyle Harrington: strings are storing storing Roi is where we're from the Fiji world, so we had been using and five, but we prefer to have the same standard everyone else's so we're happy with them fives are backing.
Martin Schorb: I am Martin, I work at the electron microscopy facility at em bl and we're dealing with the different files for different formats different scales that can range from large tiles.
Martin Schorb: Different modifications rotations light microscopy data for plan, but also very large volumes and I like to show all of that in context, so the spatial relation and orientation transformation registration that's my main interest.
Nicolas Vinuesa: hi i'm good and they worked in a place where we are working with the pathology and microscopy data images actually and we are using by formats on video from recently we're also using by format true.
Nicolas Vinuesa: So you're very interested in knowing the next file formats for cloud storage so yeah very happy to be here.
Nicolas Vinuesa: Thanks for joining.
Paolo Grisoli: hi my name is powder on Nicholas colleague at night, and yes, he said that we are starting using by farmers to grow in our tool chain and.
Paolo Grisoli: We started within five so we look forward to see what's The next step in five four months to.
Paolo Grisoli: To include it in our.
Paolo Grisoli: In our implementation so.
Paolo Grisoli: Nice to be here.
William Moore: hi i'm will more work on me team mostly on a mirror and the website of things.
Josh Moore: David and I think that's everyone.
David Gault: yeah difficult part of the meeting, have mostly been working on the bio format side of their projects.
Josh Moore: awesome so that was right at 10 minutes huge applause to everyone.
Josh Moore: yeah so I mean Deborah mentioned not being prepared, so these really aren't like about having any prepared it's it's much more just getting everyone together to talk so do feel free to just kind of pipe up with whatever you need I was going to start with a.
Josh Moore: kind of a status report from my side if anyone else has wants to do the same thing you can i'm sorry I should replace this.
Josh Moore: The link to the to the notes i'll put it back in the chat i'm feel free to start writing things under the session one notes, if there are bits you want to get off your.
Josh Moore: chest, there are links down at the bottom, so if you have projects that you want to link other people to throw it into that document, and then, when all of this is done and I managed to find time I will you know write it up on images see.
Josh Moore: That you know eventually so status update So there are a couple of things that are going on taking a step back, especially for those who are just joining, for the first time i'm.
Josh Moore: There were conversations I think that began after the I to K, the images to knowledge meeting.
Josh Moore: um where there was kind of a clear direction that yes, there was interest in Czar and in five there wasn't a lot of interest in having more and more formats.
Josh Moore: So we all decided we were going to try to find a way to work together right so that's where these calls began, and all the conversations on the on him and Jesse.
Josh Moore: So most immediately.
Josh Moore: The tsar project and only me projects received eos funding so essential open source software funding from Chen sucker Berg initiative.
Josh Moore: i'm to basically push this work forward so the tsar work was specifically on i'll talk about that first was specifically on getting to the next specification v3.
Josh Moore: um the goal of that was basically to unify the tsar and in five specs right, so they are both formats, are very, very similar very simple um and basically if we made some small adjustments, we can bring the two together so The hope is that, as our v3 the spec.
Josh Moore: will be a proper subset of all the tsar work and all the end five work right so that's where we're going um the funding is coming to an end, it was a bit rough doing all this during the pandemic so.
Josh Moore: The way it worked was the funding went to numb focus, so if anyone knows pi data.
Josh Moore: numb focus is a project that helps.
Josh Moore: Open Source projects take money and distribute them to contractors.
Josh Moore: um we did that there are a couple of different contractors who came in and out so there wasn't like a nice continuation to get the project done.
Josh Moore: um the state of where everything is is that there are branches of the specification the v3 specification their branches that.
Josh Moore: Have the tsar Python project which can read the specification there's a c++ implementation um.
Josh Moore: The implementations that haven't been done yet and may get done over the next couple of months, our Java Czar v3.
Josh Moore: javascript and I think someone began a rust implementation, so this is something we will talk about throughout the rest of the next two hours.
Josh Moore: um that, as we have more and more implementations of the specification, it becomes more and more difficult to keep things up to date so that's just a general problem that will have to think about.
Josh Moore: um from the all me point of view um what we've been focusing on our so largely again for for everyone who's joined new leading up to the to the 2020 images to knowledge meeting in December so end of November, beginning of December.
Josh Moore: We focused on storing what we call of labels I think that's what some of you will call annotations.
Josh Moore: Some people will call mask but basically having a way to.
Josh Moore: record a segmentation of your images, with some metadata and on storing high content screening.
Josh Moore: Since then, largely in 2021 we've been focusing more on a 3D use case of those are primarily to the use cases.
Josh Moore: have run into problems that I assume, others have run into when using Czar it's a problem that doesn't exist in the in five world which is.
Josh Moore: All of the chunks are stored in the same directory so as you start to have more and more chunks in your file format eventually it's I think the largest I hit was.
Josh Moore: 10s if not hundreds of millions of files in a single directory and things start to fall over.
Josh Moore: So basically and that's a problem of the specification as well, so we're kind of taking a step back, trying to fix some of these underlying problems.
Josh Moore: So we're not really actively involved with a specification right now i'm are basically trying to get the 3D performance up and do some benchmarking.
Josh Moore: If there's a next specification that we would start to think about that would be Meta data, basically, there needs to be a breaking change from from oil, these are V1 to V2 or sorry the oh point one to Point two and that's probably will we're still we will start looking next.
Josh Moore: But maybe the conversation that we're about to have will change that but that's just our general are rough roadmap.
Josh Moore: um The other thing that's driving us is that more and more we're receiving data sets that can't easily be put into a marrow.
Josh Moore: um and so even the idea, so the image data resource the idea.
Josh Moore: has no marrow underneath it, and so, if you get to the point where there's data that doesn't work well in tomorrow, you need something else we assume that something else is only bizarre and we will start then trends forming converting users data into armies are for production.
Josh Moore: which will also drive the need to have very clear milestones where you know we will support and oh point 1.2 or three because otherwise the data will get lost in it.
Josh Moore: So those are kind of our drivers and needs that we need to see happen next.
Josh Moore: um.
Josh Moore: That went faster than I was expecting that's excellent, are there any questions or thoughts about that, so I went through it super fast, so if anything was unclear.
Josh Moore: feel free to unmute and just scream.
Juan Nunez-Iglesias: I think I don't want is meant to be broken so i'm happy with that.
Josh Moore: it's good to hear.
Constantin Pape: I mean, I have some thoughts on the label specification sort of when I saw the budget more, but I don't know you want to dive into the specifics now already.
Josh Moore: Well let's let's see if there's anyone who's just kind of lost about what we're doing in general and labels is certainly on the list of specifications to spend some time on.
Josh Moore: Okay, so does everyone have a general feel of what we're trying to accomplish here.
Josh Moore: All right, and Is there anyone else from the Community who's been working on something that I didn't cover.
Josh Moore: I try to keep abreast of what's going on but.
Josh Moore: Okay, so I mean obviously feel free to throw things out there um.
Josh Moore: And, and maybe we are getting to labels, then.
Josh Moore: Constantine so there's a list of specifications listed in the document and they're all the ones I know of that someone has said they're interested in working on, so we can just go through them kind of top to bottom, spend some time on each of them to get people up to speed.
Josh Moore: If there's a handful of people who want to work on like two or three separate ones, we can just break out and actually get real work done so that's always a good thing.
Josh Moore: um and if there are more that people are thinking about and desperately need for what you know so looking at the list you know, I think.
Josh Moore: we've got everything covered a.
Josh Moore: lot I may be wrong, so.
Josh Moore: I know I mentioned anything new, at least not yet.
Josh Moore: Okay, so failing having other people want to talk let's just give the Florida Constantine.
Josh Moore: What was that I put you know a good deal of time just to go through all the specifications and then keep in mind the real goal is to figure out who will take whatever we say and actually drive it forward so right that's what we're looking for.
Juan Nunez-Iglesias: Right just intervene in the.
Juan Nunez-Iglesias: In the army fyi says support an idea and hiring and it's that.
Josh Moore: No, no, oh I want.
Juan Nunez-Iglesias: To make one that you want to skip.
Josh Moore: No, no, I didn't mean I didn't mean to skip it um yeah so we're in the process of hiring one position based in Dundee and.
Josh Moore: Two three positions based at singer for this work and are basically you know, trying to drive it from our side, if there is anyone else who has either upcoming physicians or.
Josh Moore: Someone who wants to you know get involved, we can do what it takes to have I don't know if it's a slack or a julep or.
Josh Moore: integrate people into these efforts, so we will, you know as the people finally show up these new developers.
Josh Moore: will hopefully make them known to everyone else in the Community and then make it clear this person is working on, you know X i'm and try to drive those you know, in the back of my mind, I wonder.
Josh Moore: Is that a working group, you know how formalized we want to do this, you know so far this has been very.
Josh Moore: relaxed and ad hoc, you know as long as we're making progress, I think that's fine I have been asked at a couple of meetings.
Josh Moore: You know, does is this work following some some process, you know there's a process from the rba the research data alliance, you know, or is it following.
Josh Moore: I triple E or is you know we're not following anything, yet which is OK, but you know if if people feel they're not finding a way to get involved in these this conversation, then please raise a flag or yell at us, or you know.
Josh Moore: We try to be you're raising your hand Jason.
Jason Swedlow: Just.
Jason Swedlow: The I guess the implication of what josh was saying is obviously from an odd perspective we're taking this very seriously at in the process of so less you have any doubt.
Jason Swedlow: We don't think we have the resources currently to deliver what the Community needs, I mean full stop, we do not, the challenge is too great so we're in the process of submitting more proposals.
Jason Swedlow: to grow, the team, and I just say from you know, representing all me all of those are constructed as partnerships with.
Jason Swedlow: partners, in particular, you will you sort of heard what josh was implying, for example, working with sanger.
Jason Swedlow: The ones we're working on now are actually international partnerships so looking for partnerships across boundaries, so the extent to which that is interesting to any of you.
Jason Swedlow: And it's something that you or your groups or institutions, whatever are interested in driving, please do make contact, because it would be great to do that and to do that in a way, where we have.
Jason Swedlow: I was gonna say as formal as possible and I, you know that gets into what josh was just talking about, but at least the glue between us to get this work done.
Jason Swedlow: You know, at least in terms of the teams and the constructs how the mechanisms as josh was saying, would be a completely different story so.
Jason Swedlow: that's probably my two cents, I will shut up and get out of the way but.
Jason Swedlow: Definitely, please do get in touch with you have some interest in doing that, and you, especially if you know some mechanism to get some a reasonable amount of funding and I without casting aspersions anywhere anywhere reasonable means at least a couple years and at least a couple sours.
Jason Swedlow: Sorry, just one.
Josh Moore: More funding source Nice.
Jean-Karim Heriche: All right, yep I was going to say something.
Jean-Karim Heriche: along the lines that maybe i've been.
Jean-Karim Heriche: Somewhat semi formal process might actually help in recruiting more for more.
Jean-Karim Heriche: Contributions i'm thinking, maybe something like you're the lead with some of the.
Jean-Karim Heriche: Software open source software project, maybe on our rfc based type of.
Jean-Karim Heriche: of things and.
Jean-Karim Heriche: From my point of view, I think it might help in an onboarding some of the vendors like microscopy companies so that actually they they have some people for for implementing.
Jean-Karim Heriche: file formats, so if they could actually devote some of that default away from their own proprietary format to work, something that.
Jean-Karim Heriche: is more Community based.
Jean-Karim Heriche: But I think it would help to have at least some sort of formal formal process or semi formal process for that.
Jean-Karim Heriche: And i'm also wondering.
Jean-Karim Heriche: If you could involve maybe your by imaging in here.
Jean-Karim Heriche: Maybe to mediate with the the companies, I don't know Jason probably knows more than me yeah.
Josh Moore: Well, interestingly i'm john Federico may join in the afternoon session so let's.
Jean-Karim Heriche: OK so maybe it was asking them what they think about that.
Josh Moore: i'll place that question to them when they went in if they come.
Constantin Pape: From MIT of the year, like partially funded by zero imaging to do a bit of graphic might also yeah touch touch the specs.
Josh Moore: Constantine gets.
Josh Moore: The pole position but yeah others welcome and just thinking about the process Sean cream so we'll.
Josh Moore: do some screen sharing, by the time we're done here and least kind of show what I would think would be a good way so using the NGA FF.
Josh Moore: repository but open to suggestions, so it might be that we can take the outcome of what we discussed and people who want to sign up for things you know assign a sign Constantine a task if that's what he's if he's on board and then others can can jump in.
Josh Moore: anyone else on kind of the.
Josh Moore: High Level funding fun.
Josh Moore: process yep.
Jon Fuller: So just one thing from my site and.
Jon Fuller: Maybe coming to what john cream was mentioning about bringing vendors on board, I think one thing that we've noticed it also that it's possible is if you're buying an instrument, then of course you have quite a lot of.
Jon Fuller: ways to motivate vendors to to contribute to these kind of things so that's a requirement on your side and you're about to give a vendor a lot of money, then that's.
Jon Fuller: that's an easy way to contribute to push vendors in that direction would be something that we've seen in the past, at least on our side, maybe, if anyone else is.
Jon Fuller: kind of binding instruments than that something just to bear in the back of your mind.
Josh Moore: yeah.
Josh Moore: Agreed, I mean we certainly have been telling people that for years, but I guess the question is what.
Josh Moore: What can we do so, what can this group do to help people when they're purchasing so i'm not exactly sure what that is you know.
Josh Moore: A formal statement of support for what we're doing, and you know the the vendors must sign it i'm not sure, but ideas welcome.
Jon Fuller: I mean, I guess the the.
Jon Fuller: practical thing on the side of the person purchasing is you can say you do you support this file format, or can you support this file format.
Jon Fuller: it's being the first step to that and then maybe having.
Jon Fuller: You know from there that's like the the sort of stick side of things, and the carrot might be something.
Jon Fuller: Some statement that would help a vendor to kind of say okay well how do I.
Jon Fuller: kind of make those steps to support that.
Jean-Karim Heriche: I think the one of the issue is that it depends a little bit on the process by which the microscopes are required.
Jean-Karim Heriche: So, for example, I don't have any say in in in the decision for for the microscope I can basically say well ask them if they support days but that's basically right at the bottom of the list of things that.
Jean-Karim Heriche: People would want so.
Jean-Karim Heriche: yeah I don't know if you're a facility had and you or someone in charge of making the decision, yes, but otherwise I think it's difficult and and also, I think it's.
Jean-Karim Heriche: probably better to have something that already exist when you ask for for features for for availability, so I think might be too premature here, but on the other, and maybe involving the the companies into.
Jean-Karim Heriche: Contributing so that they actually feel that they are needs also addressed.
Josh Moore: Definitely.
Josh Moore: will get there, one way or the other, so.
Josh Moore: More resources, the faster we'll get there.
Josh Moore: Okay, so shall we start talking about details.
Josh Moore: Because that's why many of us are here Constantine us start with labels.
Constantin Pape: I mean okay from from my side, so there are two points I mean the first one, which might be a bit discussion so just I mean i've been looking at the whole idea again and i'm still not sure how happy I am with this everything living sort of under one big container.
Constantin Pape: Where the issue sort of, in particular for kind of Labor or segmentation for like very big volume.
Constantin Pape: em a test right, you will only want to ship sort of the labels when they updated you don't want to ship, the whole raw data again.
Constantin Pape: And of course it's still feasible right if everything is sort of under one container, but in that case at least some of their needs to be some.
Constantin Pape: tools to help the someone who wants to do this, so that you can really just ship to the relevant part and also update the parts and the Meta data.
Constantin Pape: That do this I think if someone is just sort of presented with this folder structure and this.
Constantin Pape: That death, the raw data, and then we have these 10 different segmentation in these other sub folders and now at another one, this might be sort of a bitch.
Constantin Pape: yeah not ideal, from your perspective and mad people just might be people to just say oh i'm gonna ship, the whole thing again or just just not feasible if you have like a way to put out by passion to say well data set.
Josh Moore: So from I can't remember it was the the December color the October call, and we certainly added a issue here i'll put in the notes it's remote remote.
Josh Moore: um So for me it that falls under the concept of supporting remote links in the tsar.
Josh Moore: um yeah, so I think we I think everyone was completely on board and my reasoning, for not having done it was just starting off simple and getting more complicated, so I.
Josh Moore: OK, so I think that means there's nothing needs to change on the labels implementation from what you're saying.
Josh Moore: But you would need to be able to follow a link to a remote data set so you would have you know the original data volume.
Josh Moore: Well, actually, it probably goes the other way around, you could put as a segmentation and Azhar somewhere think so, and then that could link to the original data, and so, if you Double Click you know you try to view the segmentation you'll you'll find a way to get access to the.
Josh Moore: Data right exactly yeah.
Constantin Pape: yeah yeah I just think it was great sort of to put this into production would be pretty important.
Constantin Pape: And then the second part would be for for the version opi to to think about specifications for Meta data like especially transformations which is something we are interested in sort of this large data your data view our mobi site.
Constantin Pape: And they I think they are, I mean two proposals that i'm around one is this open organization.
Constantin Pape: Data layout and then we run, we did for one of the.
Constantin Pape: workshops for the new bias and yeah sort of their work, to the question like, how do we actually go into the process of making a proposal to to add these things to spec.
Constantin Pape: And if there are other competing proposals out there, we should be around.
Josh Moore: yeah let's actually leave so that's probably the most interesting question.
Josh Moore: So does anyone else have specifications that we should compare.
Jon Fuller: Something.
Josh Moore: else already done this work, so I go for it.
Jon Fuller: I spent a little bit of time and we've had a quick.
Jon Fuller: conversation in the form with bank it on I assume that when we talk to you about labels, I mean this is.
Jon Fuller: In the case of whole site imaging i'm thinking about a as a pathologist draw something on an image and I want to or there's an algorithm specifies something on an image and it's essentially a Polygon or a rectangle.
Jon Fuller: That, I want to them.
Jon Fuller: That has some metadata attached to that as well you know, maybe a label of this is a whatever organ organ l.
Jon Fuller: or cell and I want to share.
Jon Fuller: with other software so.
Jon Fuller: This this probably a couple of things use cases that we kind of head on our site that we thought about so one is.
Jon Fuller: That you know I I annotated something in orbit and I want to annotate that in order to view those annotations in queue path.
Jon Fuller: Maybe there's some different functionality, you want to between the two.
Jon Fuller: And then second use case it's really going down these kind of I think is quite typical into the deep learning cases where you say okay Now I want to output these labels to some arbitrary algorithm running in a container maybe some black box, essentially, I want to output some.
Jon Fuller: images and some labels and I want to then returned some labels back and view them on my image in that case, and I think for sure transformations is something that you want to be able to support in depth.
Jon Fuller: But then it's also kind of thinking, a bit about whether you want to also namespace certain bits as well, so you say well you know I I have something that actually it's probably only relevant to orbit but I namespace that and if someone else wants to.
Jon Fuller: You know use that part of my my annotation then they can, but then they're kind of down to my aka that I talked to find in the on the orbit namespace essentially.
Jon Fuller: So that was kind of what was.
Jon Fuller: done to kind of use cases a bit on our side.
Jon Fuller: Maybe I let that sink I also had a question, because my ignorance.
Jon Fuller: And so on this outside if I store as our file and on s3.
Jon Fuller: Does that exist in as a single object, or is that that's multiple objects, but just within a defined format okay great Thank you.
Josh Moore: anyone else have to add to that.
Deborah Schmidt: I have a question, yes, yes, what john just talked about is vector based labeling right and some of us are dealing with takes a base level links, I guess, and.
Deborah Schmidt: That could be a spouse or then like so different modalities and i'm not sure exactly what the current proposal is about, and I was also wondering where I can look it up just to get some stuff about my disk image slivers version 0.1 yes okay.
Josh Moore: The current yeah and it's um you know, so the the extent of what's there is in the latest version of the NGA FF spec.
Josh Moore: So there's but I don't think there's anything new that's happened that's not on that one thread Deborah so just for everyone's benefit the current extent of the label spec is.
Josh Moore: um let's take a step back, so the first back was basically how to specify and multi scale image right, so you want to have a.
Josh Moore: If if the image so coming from the army world all the images are currently five D, so one asks under the tbd section do they have to be five D, currently, yes, but that's certainly something we can talk about.
Josh Moore: um and then every five D volume.
Josh Moore: can have a some multiple arrays a pyramid of multi scale arrays for having the sub resolutions, so you know that's just an image.
Josh Moore: The only thing that the label spec does is it says Okay, you can have an image.
Josh Moore: With it sub resolution, and you can define that it's a segmentation it's a it's a labeled image and it can point back then to the original data.
Josh Moore: That currently is within the same Czar so you can have the labeled image and the original data, you have a pointer from one to the other so that's what I was talking about a second goal is eventually we want to have remote pointers and you can specify so color metadata and.
Josh Moore: annotations per.
Josh Moore: pixel value in the labeled in and the labeled image right and that's kind of it, for the moment right so to the extent that we want to do more with the pixel based.
Josh Moore: labeling we can add to that specification and then there's been several conversations around the polygons, and so we could actually maybe shift to polygons next on to kind of keep those two conversations close together and I guess meshes kind of it is involved um.
Josh Moore: You know, so what is that going to look like, so I think.
Josh Moore: There have been a small handful of proposals on the the Polygon representation so that's well known text well known binary and I forgotten the one that Anatole nested it's.
Josh Moore: it's basically a format that also allows you to store meshes would kind of bring polygons and meshes together.
Josh Moore: So I do think we want to support the two worlds and then it's kind of a question of just getting all the features that everyone wants from from each of them.
Josh Moore: Go for mine.
Martin Schorb: What about sub volumes and individual object so, especially in the cryo vm world where you identify individual proteins and a volume.
Martin Schorb: You want to just give the position of each rhizome and maybe an orientation or a state as well, and that would be the information that should also somehow.
Martin Schorb: fit.
Martin Schorb: So it's basically a list of objects with you know some some metadata for each object like orientation state.
Martin Schorb: and probably a sub volume associated somewhere else, where you can then load the atomic structure of this thing in position, so you don't need to fill the entire volume with this structure but it's like very sparse but very high detail.
Josh Moore: I mean I wouldn't say no for.
Juan Nunez-Iglesias: Some volume, do you mean pixels do you mean like a little hyper cube R cube or.
Martin Schorb: It can also be I.
Martin Schorb: Would you like to spend literally also be a vector eyes model of the of the molecule like where each atom sit like the chemistry bonds in in some spectra specification.
Martin Schorb: it's not necessarily volume data.
that's.
Kyle Harrington: The point clouds are meshes representation, I think.
Martin Schorb: In some sense, yes, but that's only it's only very sparse very little objects here in their place in the whole volume.
Josh Moore: I mean, I guess, for me, so and I may be just you know holy naive, so I guess, this is one of the things I wanted to say up front is that you know I consider you guys to be the ones who are saying what actually is valuable and needs to be defined.
Josh Moore: And it's my job, just to like get you to come to a consensus and specify it and support it for a long time right so um.
Josh Moore: What that sound like sounds like, though, to me, is is part of the Polygon specification for, for example, just being able to have a table of points.
Josh Moore: In in higher dimensional space and you were defining things and associating metadata with them, you know, there will, can be a table of data for every point or for a set of points or or right um.
Josh Moore: I think that's consistent but someone would have to tell me if that doesn't meet all the requirements.
Guillaume Gay: If I may.
Guillaume Gay: I.
Josh Moore: Just do it, I can see you.
Guillaume Gay: know my webcam is out sorry.
Guillaume Gay: So I looked a bit into polygons and Mrs this last since the last meeting.
Guillaume Gay: I think, having both in the same world is difficult because meshes are have a kind of strict definition and meshes imagine, people are expecting to see faces and vertices and that set and adding to it means bending the specifications of it, I think.
Guillaume Gay: But I think what you said that the use case where you have a a protein at a certain place, I think, a point plus Meta data pointing to ptb entry, for example.
Guillaume Gay: And then just having the whatever representation, you want from TV, I think that this in polygons basically arrow eyes or put polygons on our eyes, yes, and I think, as long as your console points and points Meta data to that location, I think it's it's better to split the two.
Guillaume Gay: The two worlds.
Guillaume Gay: So yeah that's my two cents, as for as long as then, then they can live the mind as for meshes.
Guillaume Gay: I think, p Li can very easily be written in za.
Guillaume Gay: And is a well known specification for meshes and it's really a no brainer to write a PA lies our.
Guillaume Gay: code to have meshes just like.
Guillaume Gay: easy and understandable missions for everyone.
Josh Moore: that's it for tonight thanks good young, can you give us drop a URL into the document for what you think would be easy to represent thanks john Kerry.
Jean-Karim Heriche: was going to say something a little bit along the same line but also considering point clouds So the question would be if we consider point to be.
Jean-Karim Heriche: The minimal Polygon if you want, because what I think also Martin was alluding to reset for some some points you would also associate a vector basically.
Jean-Karim Heriche: have, for example, indicating directions, or that could be indicating value so The other thing, so it could be basically numerical make Meta data on the audience.
Jean-Karim Heriche: Then, so what talking about the pi format reminded me that I don't know we haven't followed necessarily all the discussion, but if you guys have looked at the vr l.
Jean-Karim Heriche: format also.
Jean-Karim Heriche: just another way also of representing any eight is basically specification for four points and polygons and I think meshes yes i've only looked at it, a long time ago, but.
Guillaume Gay: to remember that i'm not sure it's like i'll go ahead.
Kyle Harrington: So so i'm pretty certain that poi it really actually covers all of these cases, because you can extend our betray attributes you don't have to even have faces.
Kyle Harrington: In all cases, it could just be only described vertices it can describe arbitrary numbers of dimensions.
Kyle Harrington: So you can, if you want to talk to attach orientations to every point that that's no problem.
Kyle Harrington: I mean, one of the reasons but it actually gave him and I were talking about the discussions you can store chemical kinetic information at each point anything you want it's really just a table at the end of the day.
Guillaume Gay: I had questions about hold because you can't stop you can define a hole.
Guillaume Gay: In pri or so they say in the specification so.
Guillaume Gay: That that was maybe you don't have that notion of yeah yeah.
Guillaume Gay: So maybe for for very generic.
Guillaume Gay: Li it's not adapted I don't.
Eric Perlman: link into another topic we're gonna hit here, what are the things i'm curious with the meshes is going to be multi scale and also fragments so we imagine very large meshes that could be.
Eric Perlman: Millions or even like a billion faces, how do we represent, that in this format so tied into the Multi scale so like we have meshes each of the Multi scale and then do we chunk them along the same chunks as the boundary where is this going to be sort of a parallel chunky.
Josh Moore: I have seen some.
Josh Moore: i'm trying to remember where I saw it i'll find the link and send around, certainly if we kick off the meshes conversation, again, I will add it there um Maybe it was in geosciences someone was looking at multi scale meshes.
Josh Moore: explicitly Eric so yeah So hopefully someone else has solved it but.
Eric Perlman: that's an Arab lands or has a very custom multi scale mesh implementation, which is something we could use as maybe a reference not for the format per se, but as to like what is involved.
Constantin Pape: Just off of the hard things from this i've had left, right and para who also have a pretty custom way to do with the motif specialist.
Okay.
Eric Perlman: yeah exactly between the between those we can figure out which features are necessary, I mean it sort of comes down to defining the scales and then defining how each of those scales are chunked in the end dimensional space that you have.
Eric Perlman: The hard part becomes being being the one who's actually rendering then and choosing which one to access but by having the combination there you actually get you know fast ui and interaction to these things.
Jean-Karim Heriche: And I know the soda, that is, that I was thinking is maybe if there's.
Jean-Karim Heriche: Too much trouble representing many things in one format is using linking to specific representation so again, for example, taking the example of associating a vector to a point, or you don't necessarily have to have that vector in the same way presentation, but you could.
Jean-Karim Heriche: link to let's say a table or to something so treat some of that information, maybe as.
Jean-Karim Heriche: Separate I mean it's more maybe more leaking maybe maybe at some point, it comes with a penalty but in terms of performance but might make things easier to to split things a little bit more.
Josh Moore: yeah there's definitely a.
Josh Moore: The costs, you know will start to grow exponentially if we try to do everything in one format, so I.
Josh Moore: i'm hoping that others will, for example on for tape tabular tabular data there's something called the awkward arrays project right in Python and they're working together with is our team.
Josh Moore: You know, and it allows you to store pretty complicated tabular data in bizarre you know so to the extent that someone else comes up with a way to represent complicated.
Josh Moore: data and metadata and Czar we can make use of that but I agree on agreement you know.
Josh Moore: If we have to bend over backwards to represent something or we have to redo it entire spec, then we should stop and and reevaluating right, you know we shouldn't redo all of vr ml, for example, or all of anything.
Josh Moore: I know gilliam I can't remember who you got in touch with, but you know asked can this mesh format be stored in Czar and the the developer basically said, why would you do that, you know that doesn't make sense, so there's certainly a a fine line that we have to keep in mind.
Guillaume Gay: That was the mesh io.
Josh Moore: misha misha.
Josh Moore: cheers Thank you.
Josh Moore: um okay so aware of the time, and I mean we can always look back to these.
Josh Moore: Two kind of summarizing questions for labels polygons and meshes does anyone else have a what was the word pretty custom implementation that they know up that they want to get on the list of things that should be evaluated on don't feel embarrassed.
Josh Moore: You know.
Josh Moore: Research software engineers at rest develop new formats that's just what happens um and to.
Josh Moore: Is there anyone who wants to you know put their name beside.
Josh Moore: These items and keep working on it after this meeting is over.
Josh Moore: So first any more implementations that anyone wants to throw up.
Jon Fuller: So on the Polygon sage m P threw up to GEO json.
Jon Fuller: spec I can just post a.
Jon Fuller: comment after send the link here, but there was there was what we found very practical and there's a bunch of implementations in.
Jon Fuller: several languages, which is kind of handy.
Jon Fuller: I know, at least on the Polygon side of things, I would be happy to continue to be involved in.
Eric Perlman: Something I would like to see on the Polygon side would be useful tools for extracting the associated bite values from Azhar re assuming that we are using polygons for our allies associated with it image volume.
Juan Nunez-Iglesias: That sounds fun.
Eric Perlman: polygons to didn't ask type in.
Juan Nunez-Iglesias: The risk of turning my old on a student under a bus.
Juan Nunez-Iglesias: This is this is more related to the collections thing it's still pretty custom, but but there's some good ideas in this format, but dragons come up, which is you know it's a collection of images each image has a segmentation and it would be good to be able to open.
Juan Nunez-Iglesias: Individual images with their Center segmentation or the whole collection has a thing so it's a bit of a hierarchical thing it's pretty custom.
Juan Nunez-Iglesias: But it's Nice, and it would be good to be able to do that sort of thing with armies are.
Juan Nunez-Iglesias: Moving forward and and you know I think dragon looked at the whole plate specification and whatever.
Juan Nunez-Iglesias: And it's very heavy weight, for if you don't actually have a plate right if you have some totally unrelated collection of stuff.
Juan Nunez-Iglesias: Just like you know images have been finance right that's one of the things.
Juan Nunez-Iglesias: yeah.
Josh Moore: i'm going to.
Josh Moore: Ignore you for a second one, so I mean that's a good point and I actually have a few things to add to that, but did not get us completely into collections until we've signed off on labels meshes and polygons just very briefly okay.
Josh Moore: Last call for implementations anyone else who wants to get involved young are you.
Josh Moore: Still in, or are you tired of it yet.
Guillaume Gay: No, no, I mean I mean okay.
Kyle Harrington: So we were interested, but I actually the question I would have is what's going on with the Java SAR side of things is we're in Java land.
Josh Moore: So I mean david's here and can give us more details there from our side, we will work on as our reader and writer.
Josh Moore: That means that bio formats, will be able to read and write um I think we can then bootstrap up higher separately.
Josh Moore: In bill Heidelberg has the movie.
Josh Moore: You were which has its own implementations of Azhar reader they can also read from s3 and that's the big data viewer space i'd really like to kind of combine more of those things so that we're each depending on each other as opposed to everyone's forced to develop their own.
Constantin Pape: And if I read some of our in our movie sinks, this also inherits from this outfit and five za.
Okay.
Kyle Harrington: that's that's our land as well, so yeah.
Constantin Pape: I mean, I think this is fairly competitive but it's just sort of tiny things that needed to be duplicated and following horrible engineering practices is just duplicated code, but if someone was much knowledge would look at it as a respected.
Josh Moore: For what it's worth so I was going to say this, towards the end tomorrow so every two weeks there's as Oracle is our Community call, as opposed to an old movies or Community call right it gets confusing um.
Josh Moore: that's tomorrow night at eight o'clock Central European time sorry I do your own math um I guess for kyle it's the same time zone so it's fine um.
Josh Moore: I have tried to get more of the Java Czar in five implemented years to come, so there are three that I know of, so the low level api's that's in five jays are and net CDF Java.
Josh Moore: Hopefully they'll all be there and then we can start at the bottom to build you know it properly engineered layered.
Josh Moore: code stack so if anyone would like to join you're welcome to that's tomorrow night yes.
Josh Moore: um okay so but going back to the most important part of that statement kyle I put your name I marked.
Josh Moore: you're interested that's good to know.
Josh Moore: yeah all right anyone else.
Deborah Schmidt: I will just quickly mention that I do have some experience with syfy also have this like I didn't do much there but there's anything I can help with on ease of your stuff.
Deborah Schmidt: I just know that inside we we get a bunch of issues because of Sophia or he plugins right.
Deborah Schmidt: I would really like.
Josh Moore: yeah I mean it's it's going to be interesting, so at the moment.
Josh Moore: You know, you can imagine, when we get to the point that more and more data is you know.
Josh Moore: Okay, we convince the vendors and more and more data is being produced in this format all of our tools are producing the format, you know.
Josh Moore: Things will have to keep getting easier because I do have the feeling we're all kind of struggling to work with yet another format it's the you know the X case ED.
Josh Moore: 15th standards problem at the moment, you know completely realized that um so anything we can do to make our lives easier, but you know, step by step, big thumbs up so um so do scream if you're if you're kind of suffering and we'll try to figure out a way to fix it.
Josh Moore: Okay anything else on a Polygon yep.
Constantin Pape: I do we also continue involvement with like the not and fixing white labeling spec right now.
Josh Moore: sure.
Constantin Pape: I read this is what I would be interested in looking at the sort of getting to transformations in the next iteration.
Josh Moore: Okay, so everyone so far was on.
Josh Moore: vector based.
Josh Moore: anyone else, particularly involved in want to be involved in in pixel based.
Deborah Schmidt: I think that's where I went to us to okay right.
Kyle Harrington: I mean in particularly the transform the pixel wise, yes, the transformations are also particularly interesting because we have those associated with each of our measures.
Deborah Schmidt: And what I didn't get completely from the post was to you already support mighty live like mighty.
Deborah Schmidt: mighty labels for pixel.
Josh Moore: For.
Josh Moore: pixel based labels, yes, definitely like.
Deborah Schmidt: overlapping labels that works.
So.
Josh Moore: that's certainly something that can be discussed, you know can be improved, currently there are two ways to deal with overlapping labels one is um you can have a collection of labels, so you can say that the Union of all these labels represents what we want.
Josh Moore: or specify.
Josh Moore: i'm an extra pixel value for where the overlaps are right, you can you can define.
Josh Moore: A, B and then the overlap is see right.
Deborah Schmidt: yeah because this was a big thing I can my for my lip you clip that we often discuss because we have.
Deborah Schmidt: These overlapping labels or the time and you cannot be presented in in one image, without any extra metadata like you can have a specific pixel value for the overlap, but you need to snap to.
Deborah Schmidt: This overlap, we presents these two labels, or something like that right and we didn't know how to be present, that in a file format that others would also be able to return right.
Josh Moore: yeah so you know going for it would certainly be good to get your data into the format and see which the two works best for you so.
Josh Moore: we're possible if we don't have to support multiple solutions for these problems, you know someone was asking about the minimal specification so.
Josh Moore: Try to keep the fewest number of things on the fewest number of of Sub specifications and then, if we need to add more in the future, we will like you know, for example, I don't think we want poi and vr ml, so we should choose like if we're using one of those do we should choose.
Josh Moore: One and go as far as we can with it.
Josh Moore: We may reach a point where we need to support multiple things but it's it complicates your your code, which is what we're trying to prevent.
Josh Moore: An example of that is an image is always multi scale, even if there's just one resolution just so that you don't need an if statement every time you're reading the image right, so the extent that we can just do things the in a uniform way I think it'll make our life simpler.
Josh Moore: But we'll get there.
Josh Moore: Okay transitioning to collections on the bit I wanted to add.
Josh Moore: One and drag is that I know, so I assume you read on the thread I think he'll be here in the afternoon, which isn't very useful for you.
Josh Moore: i'm Christian Fisher, and I assume Martin you're involved in this i'm are interested in a collection specifications, so I would assume they would add their name um.
Josh Moore: I i'm assuming that quite hardly and I will push um So if you have something you want others to look at that would be a good next person to look at it.
Josh Moore: um and I think the collection specification, is one that can be done pretty independently, so I don't see any reason why it can't get in super fast like you did your label specification So for me the floor is open.
Josh Moore: doors open windows open, you might just see if if you can get feedback from anyone else who's here on on feature requests that you know that need to be integrated.
Josh Moore: So everyone, I mean one kind of went over what collections are about its bags of images and with whatever metadata you're interested in so.
Josh Moore: Anyone.
Martin Schorb: I assume you would generalize that and would also include meshes finery labels also as part of a collection, because that would then go to what what Constantine was asking that you kind of modular eyes things, and then only update.
Martin Schorb: Like one part of one module of this like one new segmentation, for example, without touching the rest.
Josh Moore: yeah I mean.
Josh Moore: I don't see any reason not to do that so.
Josh Moore: I don't know enough about what the mesh you know, whoever does the mesh specification I guess we'll see but currently labels are images therefore from in my thinking, if you have a collection of images, yes, it could definitely be a collection of labels right.
Martin Schorb: yeah, the question is, if you do if you do collection of entities and entities will also include measures like a level above basically.
Martin Schorb: I don't I don't see a conceptual difference there.
Juan Nunez-Iglesias: yeah I think for me to really nice feature in in tragus pseudo spec is is the ability to open individual things as if they were the whole thing.
Juan Nunez-Iglesias: And I would hope that whatever spec we come up with has that property.
Constantin Pape: Do we do we have a link.
Draga Doncila Pop: To that proposal somewhere.
Draga Doncila Pop: So I can definitely add a link to these notes that's not a way it's you know custom is definitely a stretch.
Constantin Pape: For it.
Draga Doncila Pop: it's basically something that arose out of a need to.
Draga Doncila Pop: support both opening an associated sort of you know bag as a good word for images for labeling but training purposes, but also then wanting to maintain a clear correspondence between the individual images and their individual segmentation.
Draga Doncila Pop: I guess a future inspection and also for future you know editing so I guess that sort of speaks to what you were talking about as well about the modularity and whether like one big container in sufficient.
Draga Doncila Pop: For example, when we were working on this and the power of one of the issues was that once you opened.
Draga Doncila Pop: up a folder of images as a stack then they just sort of State A stack and so you know, to save them out into individual images again you sort of had to you know slice through that stack and ideally you'd be able to as one mentioned have a hierarchy what you can open.
Draga Doncila Pop: The stack itself or just individual images and.
Draga Doncila Pop: yeah I don't see any reason why it should only be supported by images, I definitely think that the collection of entities makes sense, definitely when I was working on this, like quasi spec the idea of having like points layers associated with images also seem to make perfect sense.
Draga Doncila Pop: And then I guess in a sort of tangentially related discussion.
Draga Doncila Pop: about the like spec being lightweight bottom up, and the five the hard coded requirements.
Draga Doncila Pop: It would definitely be nice to be able to abstract a lot of the I guess metadata that's not needed away because.
Draga Doncila Pop: What we found especially watching last year as well with remote sensing data is that Oh, and he was almost absolutely perfect to store these satellite images, but just not quite, and so there probably is I guess room for.
Draga Doncila Pop: I guess.
Draga Doncila Pop: I know amy's aspect that's further up in the hierarchy and defines even more of a bare minimum than what it currently does.
Juan Nunez-Iglesias: If that makes sense, I think one of the things that drug and I discussed earlier today is, you know if you go to do means our spec now like the draft page.
Juan Nunez-Iglesias: there's just so much stuff there, and so, if you're someone who's like trying to figure out.
Juan Nunez-Iglesias: Can I store my data this way you'll just come here and you'll go like Well, this is not for me you wouldn't say, can I can I shoehorn my data into this i'm going to do singleton dimensions for time and.
Josh Moore: So.
Juan Nunez-Iglesias: which might be yeah.
Josh Moore: i'm laughing because this is, I feel like a.
Josh Moore: redheaded stepchild i'm sorry Jason i'm.
Josh Moore: So.
Josh Moore: i'm.
Josh Moore: So, going back to when we first introduced are needed the Multi scale representation, so I went to this our Community.
Josh Moore: Open up issues said, you know I really want to you know have this extension to what you're doing just want to be able to represent, you know multi scale data on kind of went back and forth get input from the Community and, eventually, they said yeah.
Josh Moore: This is, this is, this is an art thing go, you know go do this in your own space I go over here I create the olympians our implementation, I do the Multi scale specification.
Josh Moore: And now on say Oh well, we don't want it here send it back the other.
Juan Nunez-Iglesias: No, no, no, no, not the Multi scale is fine.
Sebastien Besson: Actually.
Juan Nunez-Iglesias: It wasn't all right thing.
Josh Moore: yeah, but I think what you're saying so So how do we solve it So what does the naming look like you know I think what you're actually saying is you want.
Josh Moore: You know you're interested in a specification that lives within gfs as opposed to with the oil me metadata because I think that will me is going to continue to be more.
Josh Moore: My car microscopy based.
Josh Moore: We need to find a whole bunch.
Josh Moore: Of the other things.
Juan Nunez-Iglesias: Yes, I would like an NGO that has you know, because the thing is it doesn't have like a physical size, so it would be nice to have and I don't think there is even scope women for that.
Juan Nunez-Iglesias: And so it would be nice if.
Juan Nunez-Iglesias: The metadata can be defined minimally enough that people know.
Juan Nunez-Iglesias: You know how to specify an image with the scale without having to deal with five dimensions or things like that, and how to specify collection, without having to deal with plates and wells, and things like that.
Juan Nunez-Iglesias: yeah.
Juan Nunez-Iglesias: And I am draga do you have that folder structure handy, would you be able to share that because I thought that was very compelling earlier.
Juan Nunez-Iglesias: yeah.
Juan Nunez-Iglesias: Is that is that.
Jon Fuller: Maybe was.
Jon Fuller: was a struggle sits at the screen share just to check I understood that I think I can probably have a similar opinion and the idea would be of, from my perspective would be that if you have a.
Jon Fuller: Whole side image which is probably two dimensional and that you only want to actually care about those two dimensions.
Jon Fuller: And you don't want to care about the extra stuff.
Juan Nunez-Iglesias: You don't want to worry about i'm going to have a singleton time dimension, you want to just.
Jon Fuller: have your kid just to be done for you yeah I think I would probably appreciate that.
Josh Moore: So I think.
Josh Moore: For me, that.
Josh Moore: That that is part of all of these are you know we don't need to find a new home for that that just needs to happen, you know it's a um.
Josh Moore: I don't even think it's a breaking change because it just kind of loosens what the clients can expect, so you know.
Josh Moore: Again, going back to how do we make this practically happen, you know, starting with fewer assumptions means you can just get your client code working and get things out into the into the Community but.
Josh Moore: Eventually, we need to support more of these use cases and you know 2d is definitely one of them.
Josh Moore: You know, finding another home for something like the entire hcm or the you know the very kind of particular use cases um have to do some thinking about what the naming there is, but the the feedback has definitely been taken on board sorry go for it try.
Draga Doncila Pop: yeah so the you know basic ideas you might have input data that just looks like a bunch of.
Draga Doncila Pop: You know, leaves, for example, and you might want to annotate these now if you can open these as a stack obviously and the I guess desired behavior that we would have is, you would have a za.
Draga Doncila Pop: Bear with the specification businesses in its infancy, but the idea, rather than being multi scale levels, the numbers here correspond to the slice in the stack that.
Draga Doncila Pop: You were labeling and and inside each slice is all of the you know images labels I guess points meshes whatever else might be associated with a particular image.
Draga Doncila Pop: At that slice level and the hierarchical aspect is that you can.
classic.
Draga Doncila Pop: said so, the idea is that you would be able to open the labels Liz and the image stack itself, but then you're also able to go in here and open just one individual slice.
Draga Doncila Pop: You know, make some annotations to that save that out, or you can even go further, within and then just opened me a one particular image.
Draga Doncila Pop: Or the associated label in a slice and so that's the hierarchical structure and i'm not you know I don't i'm not a user necessarily of I guess.
Draga Doncila Pop: These tools and i'm not particularly familiar with you know microscopy or many of the I guess formats that are out there, but this seems widely enough applicable.
Draga Doncila Pop: That it's something that we probably would want to support, at least in yelling in some variety.
William Moore: that's essentially what we did with the current ACS spec right, and then you can go into the you can bounce down through your folder hierarchy down to the well and open an individual image and the labels that are associated with it will be.
William Moore: shown you so you can open just one in each.
William Moore: At a time.
Juan Nunez-Iglesias: That angels will say.
Juan Nunez-Iglesias: there's a there's a hierarchy which is.
Juan Nunez-Iglesias: plates and wells is that is that right, and then.
Juan Nunez-Iglesias: I guess yeah what I would say, is to make that option on I that's probably in your roadmap i'm not sure.
Josh Moore: Well yeah I mean I think what we want is actually.
Josh Moore: I mean, we would have done it, but if dragons doing it all the better, you know take whatever specification and then back port forward port, you know refactor the hdfs back to make use of the collection, you know so that's it.
Sebastien Besson: It should be particular implementation of whatever you're doing it's a super type thing that corresponds to specific acquisition modality, but as far as I can tell there's there's nothing in what dragon just presented that fundamentally conceptually clashes with what he does.
Juan Nunez-Iglesias: yeah awesome.
Josh Moore: yeah and you know if someone so another one that is needed, certainly is the on the tissue use case, so you have a large issue you have images that are laid out, and you know kind of a very.
Josh Moore: um exactly an orderly so someone just sent me tma.
Josh Moore: Thank you, someone said that publicly um you know representation and each of those images has a transform to get everything.
Josh Moore: represented properly, so you know if if that's what someone is already doing themselves, then it would be good to make sure that their collection representation works with draw draw goes works with the hts one.
Josh Moore: And we'll just kind of keep adding these probably the same thing for the em use case that Martin was talking about it all just comes down to you know the same kind of stuff.
Juan Nunez-Iglesias: cool.
Josh Moore: Anyone yet go for it.
Juan Nunez-Iglesias: Oh, that was just cool.
Josh Moore: Has anyone else been doing this in the background secretly well, is it pretty custom implementation, they want to talk about sorry bespoke know we can you get a terminology, right here.
Josh Moore: Go for it man.
Martin Schorb: i'm not sure if I got that right, so what What you said is that you don't want to have this scale draga sorry that the scale shouldn't be the at the top level because of.
Martin Schorb: comprehensiveness of the of the hierarchy.
Martin Schorb: Did I get it.
Draga Doncila Pop: Oh yeah, no, no, no, no, so sorry i'm definitely happy with the Multi scale like specification, you know exactly the way it is the.
Draga Doncila Pop: The difference there was just in this particular implementation for the purposes of the reader and writer plugin which particular user asked for.
Draga Doncila Pop: Those numbers represent the slice of image or more correctly an individual image which would be part of this new collection specification.
Draga Doncila Pop: And I don't see any reason why they would have to be numbered I mean i'm sure that we could you know, come up with a way to name them more usefully or you know.
Draga Doncila Pop: I don't know some sort of a zero dot zero.
Draga Doncila Pop: So the situation, but I definitely have an issue with the Multi scale implementation, the way it is.
Juan Nunez-Iglesias: Now, at the bottom of that hierarchy, you can have the Multi scale, with the single scale ish that that makes sense to me anyway.
Draga Doncila Pop: or the other way around, I suppose, whichever way we decided this morning.
Juan Nunez-Iglesias: The other way would be a bit trickier to because you wouldn't be able to have a single image right if you if you have the scales.
Martin Schorb: Do you think that you could just define that in the collection definition at the very top like what layer represents what.
Martin Schorb: The most flexible that in the collection definition.
Martin Schorb: You define.
Martin Schorb: know how your how your folder hierarchy what what that represents.
Juan Nunez-Iglesias: yeah but the point is, if you have a multi scale image like one of the design requirements is to be able to open a single image and that collection.
Juan Nunez-Iglesias: And so you can't put the Multi scale information at the top.
Josh Moore: So i'm not several you fast enough to bring up or will bring up a the metadata for the hcl specification the lock that points to the images.
Sebastien Besson: That was figured out that we had during the Ah yes, surely had a lot of.
Sebastien Besson: A lot of back and forth from executive is problem of where the metadata should live, it should be at the top level at the at the bottom level and.
Sebastien Besson: Well, surprisingly you're fine good argument for both which is down to exactly what dragon want, I want to image and an image by myself well so that data should get.
Sebastien Besson: in depth and or I want to open for collection, so I actually want to have as much into detail the top level as possible, so.
Sebastien Besson: it's a tricky balance and just is showing you and will take over of defining where the Meta data leads that contains everything and very suddenly the step of being able to reconcile all the metadata at the different levels.
Josh Moore: So we went back and forth, I think we did three or four different versions, where there was one version, where all the metadata like a a json block was at the top level with a link to every image and that kind of got unwieldy, you know so that it's definitely a balance between.
Josh Moore: You know, taking all the metadata that you're talking about Martin your where you you open up the collection, you know everything and that that the user would need to click twice to get somewhere.
Josh Moore: um we chose for the https, to say the user needs to click twice to get down to an individual image um but that may be just a special.
Josh Moore: You know implementation detail of hdfs because there are so many layers of the hierarchy, you know, in a standard collection I assume you will want.
Josh Moore: You know, and this is the type of block that we may want to standardize you will want a a top level thing that says here's how you get to the things that are multi scales right.
Josh Moore: um and then you know if a user clicks on that.
Josh Moore: Because what you what I think what we found and will can correct me if you don't want.
Josh Moore: The client to need to go and do you know lots of look ups to figure out what images to show the user you kind of want to go tell me what i'm opening opening you know and everything else, at least when you start to get into large numbers becomes very, very painful.
Jean-Karim Heriche: So, seems to me that.
Jean-Karim Heriche: Maybe maybe i'm wrong, but this discussion reminds me of some discussions i've had about designing your database and how to relate the different items and.
Jean-Karim Heriche: And, basically, the way it works is that you basically build.
Jean-Karim Heriche: relational tables that relates your your indices, so you need to have index so you're working here without index so you're getting to your data directly by looking for the Meta data that gives you where you need to get the data.
Josh Moore: And it is a design decision, how much redundancy you build into it right, because all that means you have to keep up you know if you.
Josh Moore: If you delete a well, then you need to go through all the structures and figure out everything that references that well and get rid of it yeah I mean it's.
Jean-Karim Heriche: that's the that's the problem with relational data your you have relationships, you have things that are.
Jean-Karim Heriche: that are linked to each other, they sings points to this image with this Meta data, and you have to keep these together or linked together, so you have to find the balance by between what you keep together and what you what you link.
Jean-Karim Heriche: And, and as I was mentioning at some point somewhere that you will need indices, you will need to index some of the data structure for efficiency.
Jean-Karim Heriche: So maybe you can split some of these things and work out of an index stable or or more than one.
Jean-Karim Heriche: And, and so all these things could be very efficient data structure.
Jean-Karim Heriche: I mean just an idea of following that discussion that's my understanding of it, where it's getting getting.
Josh Moore: And it may be that we can well, there are a couple of ways.
Josh Moore: I assume, initially, we will need to just think about what john crema said, every time we build a spec you know, we had to do it for the hcm the collection speckle have to do it.
Josh Moore: It may be that we can generalize some of this so that there's you know, there is a image index built into Czar or maybe it's a layer higher you know and we build services that.
Josh Moore: Keep the stuff in mind, and if you know if opening your Czar on s3 is just too slow, then you turn on whatever the services that does the indexing.
Josh Moore: kind of remains to be seen.
Josh Moore: anyone else, want to add anything to the collections discussion so.
Kyle Harrington: One thing that i'm trying to understand a bit so part of the issue with collections is at the at the root level, you might have some metadata, it has to apply to the children when you open a child, do you need to have.
Kyle Harrington: be able to get that information and how do you find it so i'm still, after all this not really clear what's the like proposed way of dealing with that.
Josh Moore: So, at the moment, so what at least the hcl specification there you know, there are three levels there's the plate the well and the image level roughly their details, but whatever i'm.
Josh Moore: plate links you to the well well links you to the plate, and the images images links you back to the wells.
Josh Moore: Right, so you so basically bi directional.
Josh Moore: pointers at each of the levels.
Josh Moore: And that's so that all images aren't registered with the plate.
Josh Moore: Right, so if you have to do a two level lookup so it's a collection of collections, which I guess goes back to martin's point of.
Josh Moore: You know, we should we should be able to have collections of anything so in this case we have collections of collections that's the design decision that we made.
Josh Moore: You know, we could roll that back and say no actually a plate should be a full collection and then it would have all the will metadata and all the image metadata all you know all in one go it's that would be valid as well.
Jean-Karim Heriche: I would, I would say I would favor the model where you can ness collections, because the experience shows that you often need these kind of nested structures so flattening might have some advantages, but I think it it loses some of the flexibility, you have when you do I bought one SEC.
William Moore: yeah I guess for the plate we didn't nest too well nesting arbitrarily depth wouldn't make it harder to give an overview of what the what the plate looks like you know you want to be able, quite quickly find.
William Moore: An image to show you for that well and if if the well happened to be have a collection, then you didn't you need to keep iterating a different depth reach so so in at least in that high contents, meaning that that would be harder but yeah it would be more flexible.
Josh Moore: anyone else on collections.
Josh Moore: You have what you need dragon.
Josh Moore: Okay, so knowing we only had about half an hour, and I would like to look at the github repository a bit there any of the other specifications that we didn't touch on that anyone's just dying to.
Josh Moore: Talk about in detail, other than that they want it it's clear all specifications are wanted by someone as quickly as possible so.
Josh Moore: I take that as a given.
Constantin Pape: I just have one procedure, a question so say I want to make a proposal for labels or image spec be to read do I do this now.
Josh Moore: yep that's what I want to end with so definitely won't forget that.
Josh Moore: Shall we just moved to that you guys are always asking the next thing I want to talk about it's great it's just like it just keeps going.
Josh Moore: Okay, I want to make sure no one Okay, so no one's screaming about any other specs.
Josh Moore: Going once.
Josh Moore: awesome okay let's do this, we can always like circle back.
Josh Moore: Oh okay so here's what i've gone through a to a more or less.
Josh Moore: significant degree.
Josh Moore: let's see share.
Josh Moore: So.
Josh Moore: Sorry that's not working.
Josh Moore: Okay, so someone mentioned the the labels specification multi scale image labels one.
Josh Moore: um, and so this kind of kicked off the conversation um.
Josh Moore: And I think only the original multi skilled thread actually got a lot of feedback, so I haven't had a lot of success since then.
Josh Moore: um so both on labels and on hdfs it kind of felt like the Community was going yeah just do what you're doing will will follow suit, which was fine you know that's that's okay um, but it is certainly about driving as much.
Josh Moore: Getting all the disagreements out of the way as early as possible, why does it keep happening um so i'll show you where that did happen and for whoever wants to specs.
Josh Moore: So it's issue 50 So this was the originals our spec work.
Josh Moore: And this went back and forth for a couple of months, you know, and if it works better on github, I guess, I would say, feel free to do it on github as opposed to image sc I try to keep the two.
Josh Moore: apprised of one another, you know but wherever you're managing to get a conversation going do it, and as long as it's on one of those two that's fine um.
Josh Moore: And then, at some point here everyone who participated will remember it started to get into the weeds of.
Josh Moore: How do we represent the Multi necessary, not the Multi scale, but how do we represent the offsets and the position and the grid size and some of the scale information.
Josh Moore: And so, at that point, I just kind of drew drew a line and said okay we're not dealing with that anymore that goes to the next spec.
Josh Moore: So I just want to get that out of the way up front that that's also part of the job is going, you know i'm only going to focus on this much i'm going to help you to you know get to a consensus here and we'll deal with the next bit following that.
Josh Moore: So.
Josh Moore: Once you've kind of driven that conversation, so you know, in this case I would kind of assume you know she posts what she has now in some kind of json representation shows some data sets um.
Josh Moore: And then, wherever that needs to take place that's fine, but I would assume, eventually, it needs to turn into an issue on the N G F F board I assume I hope the dark github.
Josh Moore: style is actually visible over zoom so I find it a bit hard to read um.
Josh Moore: So that would be a pull request against.
Josh Moore: n G F F.
Josh Moore: and
Josh Moore: It would be against latest, so this is currently written in markup called bike shed it's from the w three see.
Josh Moore: The github actions generate the html and everything from this so it's basically just markdown that you can follow on your own um it has some additions for for writing specifications, so you can have a table of definitions, you can have.
Josh Moore: links to other versions of the specifications so anyone who's written a specification, it has you know some of the markup to make it easier, as opposed to meeting do everything in markdown yourself.
Josh Moore: Currently it's all in one file um so we may start conflicting with one another, and if that happens we'll figure out what to do that, you know we'll probably have a multi level specification, which probably gets one what he wants is there's they.
Josh Moore: Of course specifications and then there's.
Josh Moore: You know hts which one can ignore um.
Josh Moore: That PR gets opened.
Josh Moore: And then there should be kind of a period of feedback from the Community.
Josh Moore: i'm MIA culpa I failed to do this, for it okay and sorry this was a conscious decision, and I will do better in the future.
Josh Moore: Basically, the meeting was coming and I wasn't getting feedback on labels and on hdfs, and so we just said okay we're merging this so that's completely known and.
Josh Moore: I will take the bullet for that, so if anyone does have something in those specifications that they hate and it's my fault, and we will fix it in the next version i'm completely valid, but to the extent possible, you know, we really should give everyone time to.
Josh Moore: To have feedback um and to have as many implementations produced for the specs as possible, so that's been the hardest part um so let me go back to the roadmap, and this is just kind of an idea on how we can make this work.
Josh Moore: So this is a github project board for the NGO FF repository um it's called roadmap it's project number one.
Josh Moore: it's linked from the notes, but i'll link it again.
Josh Moore: um so I guess my proposal would be that anything we want to work on so anything that we discussed today, anything that we talked about an image sc or, at any of the Community calls shows up as a card on the roadmap board, this is kind of following if you've not seen it before.
Josh Moore: Get hub project itself has quite a nice roadmap and i've tried to follow that and they just kind of have like all these great colors and things are just like you know, so this is what I see happening right but I need your help, I can't do that myself um.
Josh Moore: You know, put your will put your names on it, you know so.
Josh Moore: I hear coming out of this meeting that we have at least three or four cards that need to live here, they need to have your names on them and um something we haven't talked about a general feeling for when you want to get them merged into the main line right.
Josh Moore: um I don't know how far we want to look, you know, this goes through summer so June of 2021 if someone's planning farther that's fine, we can plan as far as you want in the future.
Josh Moore: um and then the question is what's the bar does it says suffice to have one implementation for a specification, or do we have a set of implementations which must support.
Josh Moore: A new spec before it goes in so concentrate i'm kind of thinking of Czar implementations as a model, you know, so we we take whatever language, whatever implementations we want to support only means our bio formats our reader big data viewer trevor's is rj s whatever.
Josh Moore: And we'll run them through a test suite before we merge.
Josh Moore: thoughts objections extensions.
Constantin Pape: Okay yeah I think that sounds good just sort of where the issue left but it wouldn't be in this on E and F.
Josh Moore: Currently that's where they live.
Josh Moore: You can link elsewhere if that's useful but I, I think, having in one place is the.
Constantin Pape: Best yeah I think that would be better than getting those are.
Constantin Pape: specs involved right, which are, I think.
Josh Moore: yeah that didn't work so.
Josh Moore: I wouldn't do that.
Josh Moore: And everyone so that would mean anyone who's interested can follow this repo should be able to know what's going on.
Josh Moore: I will keep reporting on images see so you know we'll have that bi directional link.
Juan Nunez-Iglesias: Is there, how does one get I guess make the issue to get guidance on.
Juan Nunez-Iglesias: Realistic timelines and consensus because, like you know, to take the scale one as an example.
Juan Nunez-Iglesias: I just don't even I don't even know what you're thinking and and also you know, in terms of the spec.
Juan Nunez-Iglesias: For me, I feel like it's blocking that it's the TC see ya next thing right now and that.
Juan Nunez-Iglesias: The metadata the scale Meta data would have to be somehow tied to that.
Juan Nunez-Iglesias: And I would prefer it wasn't.
Juan Nunez-Iglesias: And so, then yeah so then.
Juan Nunez-Iglesias: Variable number of dimensions, would be an issue that I would make.
Juan Nunez-Iglesias: And then.
Josh Moore: And we do also work on the implementation of the spec change.
Juan Nunez-Iglesias: What does that mean exactly it means adding to the spec and then adding to say armies are pie, because I would that mean.
Josh Moore: Well, I mean to some degree i'm I guess i'm almost less interested in the help on the implementation so that's very welcome, I mean, I think.
Josh Moore: The thing that has to happen first for each of these is really the naming conversation like you have so let's just let's just take this as an example, because the one that.
Josh Moore: The one that i'm one's talking about it's actually fairly simple and it's just a matter of doing it so in multi scale so let's see let's see where does it say five D.
Josh Moore: You know so basically this says.
Josh Moore: You know, it must be five dimensional chunks right.
Josh Moore: So the first question is.
Josh Moore: So this probably so you need to if you're going to change something like this, you need to decide, are you supporting the old version, are you having a breaking version.
Josh Moore: If you want to get your issue done and implemented as quickly as possible don't do it in a breaking style right, I mean that's kind of obvious, so you know I would think what you would do is say.
Josh Moore: You know in you probably do it down below, but you would say something in the text, like if there's not a key dimension order on the array metadata then assume it's five D TC why.
Josh Moore: The wire right.
Josh Moore: If you do find the attribute named whatever dimension order then interpret it this way right, and so, if you can write that up in English that other people understand and everyone's fine with it, then we start looking at the implementations.
Josh Moore: someone's got birds.
Josh Moore: anyone else, seeing how they can fit into this, an issue they want to create and or better implement.
Constantin Pape: I mean i'm so i'm working on an issue for this transformation, I can just share it after so let me take and then everyone can critique.
Constantin Pape: The other thing is, I mean maybe a bit specific about the master this sort of allowing nested is their initial already because I think, for us, which will also be pretty critical.
Josh Moore: So there's not even an issue, yet, for they create one for collections.
Josh Moore: know, so I think the conversation on collections didn't show up as an issue, yet so that already needs to happen, so if someone wants, you know, I was kind of guessing draga would do that so um and then.
Josh Moore: I don't know I assume nested in this can take place within that one issue, maybe we need another I.
Constantin Pape: Think it's a different fun right because it's not about collections, but really about the underlying container.
Maybe.
Kyle Harrington: you're talking about the flat just flat versus nested directories.
Constantin Pape: Exactly yes.
Constantin Pape: For the chance.
Josh Moore: That yes.
Constantin Pape: Yes, and no because that's the part nested storage already.
Josh Moore: It doesn't I know so i've had to open several PR is to get all this to work so zarin jobs are both broken across the board for nested chunks of me.
Constantin Pape: But I mean for me the nested storage yada yada.
Constantin Pape: that's usually so.
Josh Moore: So sorry in five works in five nested on s3 doesn't work geez are doesn't work as our Python fs store doesn't work.
Constantin Pape: And I think there's I pisces one okay.
Constantin Pape: yeah okay.
Josh Moore: But if you, you know if you want to create an issue go for it um and I will link all the stuff I know you're right it desperately needs to happen and.
Constantin Pape: You know.
Josh Moore: And at least that's what i'm fine with doing the implementation yeah so cuz i'm that's where i've been suffering.
Constantin Pape: I guess i'm using my own stuff too much for this.
Josh Moore: yeah if your solution is use the fly for everything that okay.
Eric Perlman: It seems like this has been this is starting to boil over and needs to be addressed by late because I definitely there's been situations where i've used and five instead of Czar based on the pair of tools and languages, I was using.
Eric Perlman: Like I need to Amazon with soulful tools so it's good to be and five on aws.
Josh Moore: yeah that that's kind of the root of all evil at the moment, so if we can fix that that'd be great.
Constantin Pape: Okay sorry this is again a bit unrelated but just because I have these implementations do you think we should maybe much a bring this entity that developers umbrella, because I feel like i'm a bit I mean i'm happy to to work on this, but I think, maybe there should be some.
Constantin Pape: sense of responsibility for it.
Josh Moore: So my you get big thumbs up for me, so I think it's great i'm.
Josh Moore: In general I think this goes for the tsar developers organization and for the oil me organization, you know, to the extent that anyone wants their code to be official.
Josh Moore: that's great you know we love you know you guys are doing great stuff if you want to move it to the org that's fine you probably won't hear anyone say you know, and I thought this about your so can someone paste this our implementations repository please um.
Josh Moore: I fought several times, I should really tell Constantine just to move it to the org.
Josh Moore: But that feels like a very dodgy thing to do, as an org Member, you know you don't feel comfortable going to someone that you know you really should, though.
Josh Moore: I think both of the organizations and, probably, you know, we could say the same thing for Fiji and for all of our party organization if you've developed something that's really cool and you want it to be an official project go for it like you know make that happen that's that's wonderful.
Josh Moore: you're also welcome to just keep it as your own if you know.
Constantin Pape: Making an issue and tagging the relevant people fight.
awesome.
Josh Moore: yeah and I definitely think we need something like that, for me, Czar as well um I don't know if we just copy that repository or if we if anyone has ideas on on how they would want to do that speak up.
Josh Moore: Okay i'm going to look at my list of things that I wanted to say.
Josh Moore: If anyone else has anything they want to add feel free.
Guillaume Gay: Just to make sure.
Guillaume Gay: So far, the mesh if.
Guillaume Gay: The correct workflow is, first, the specification, then the implementation so I should have been an issue to specify how to store meshes here.
Josh Moore: So.
Josh Moore: Help them recover couple of questions built into that so completely feel free to open an issue that would be wonderful to so big support um.
Josh Moore: To be completely honest, you know I we probably don't always do this specification, first we often start with you know the that at least one implementation first just because you know we're human um but you know it.
Josh Moore: A specification should come with one implementation and generally maybe maybe i'm wrong i've found that by pasting a very simple snippet of json.
Josh Moore: people understand what i'm talking about better, you know that that seems so a screenshot saying this is.
Guillaume Gay: cool.
Josh Moore: And here's the way I want to name an end json gets gets a lot of people involved so that's what I would suggest, but feel free to play around with it i'm.
Josh Moore: You know.
Josh Moore: we're all new to this.
Jean-Karim Heriche: But I, I agree with josh I think the specification should come with a reference implementation because of a specification always as ambiguities and the reference implementation basically takes care of that it, it shows what actually is meant in when it's a big years.
Jean-Karim Heriche: And it can be used for testing all the implementations making sure that they do the same and the top with the specification, the same.
Guillaume Gay: Okay.
Josh Moore: anyone else have anything they want to.
Josh Moore: throw out there.
Josh Moore: shouldn't be that mean to look critical.
Josh Moore: So I think the last question from my point is whether or not anyone feels that needs to be anything different or more frequent or whatnot in terms of communication.
Josh Moore: um I think the standing agreement is that every you know roughly once a month will have one of these calls i've kind of failed and it's been more like every two months, which actually has felt okay as well, but if I plan on every month and I actually make every two months happen um.
Josh Moore: It may be that if more people are building the specs will need to talk to the people who are actively working on trying to merge into the main line will need to chat more often I would leave it to each of you to just raise a flag, when you want to chat and we'll invite whoever.
Josh Moore: um.
Josh Moore: Can formalize that if we want, but I figured that's yeah.
Jean-Karim Heriche: Do you have a chat channel some something for for people will will actually get their hands dirty on the on the specifications on the implementations where they actually can.
Jean-Karim Heriche: Directly get in touch with each other, without necessarily going VI issues or us who image see.
Josh Moore: I don't know so good question very good question and open to opinions, the two things I know of, and if anyone wants to suggest more ones already smiling i'm.
Josh Moore: The first would be github discussions I don't know if anyone has had good experience with those um.
Josh Moore: Certainly, for Czar it doesn't tend to work, you know, so I don't get much feedback when I use the Czar discussions.
Josh Moore: But if everyone is watching a basically a github discussion looks like an issue but there's no assumption that it's an issue it's just it's a place where you can chat so.
Josh Moore: that's one option, the other option which i've proposed a couple of times so one time, I proposed it formally, which was a separate julep.
Josh Moore: Beside the image se discourse, because sometimes you just need chat um there wasn't a general acceptance of that from the administrators of the discourse, which is fine.
Josh Moore: Since various rogue people like one have suggested it again and again, and so there is an image se julep I don't mind using it um but it kind of yeah that requires a larger decision.
Juan Nunez-Iglesias: On there if people want to.
Josh Moore: Like I said.
Josh Moore: yeah well yeah.
Josh Moore: i'm not guilt free it's.
Josh Moore: Well, if github discussions work I think they're.
Constantin Pape: Not sorry I.
Juan Nunez-Iglesias: Get her.
Constantin Pape: Get her.
Josh Moore: I get her, I think the threading on guitar is still very painful I can I can never find or follow the threads on guitar and the one thing that zoom does really well.
Josh Moore: much better than slack or anything else is named conversations you know so every thread is clearly named and you know what you're talking about and I love that.
Juan Nunez-Iglesias: You know so.
Josh Moore: For example, when it comes to the party zoo look like I only.
Josh Moore: Read the ones that have all me and the title and I ignore everything else.
Kyle Harrington: Whereas like worse than.
Josh Moore: Someone faster than me.
Josh Moore: Oh.
Josh Moore: would have been fine my screensaver came on anyway.
Josh Moore: So we can try it out, we can veto that though so that's that's the that's the.
Josh Moore: pirate conversations.
Josh Moore: Basically i'll respond to any CC anywhere so just.
Juan Nunez-Iglesias: It does it does have premier links as well with the caveat that you do need an account, and you have to you can sign in with github or whatever, but it does.
Josh Moore: anyone else have a preference or a suggestion for a place to do this, so my first example of a project, leaving get her to go to discord this morning I was like Oh, my goodness.
Juan Nunez-Iglesias: I will.
Juan Nunez-Iglesias: send me advertise the thing that i'm working on, but hasn't caught off the ground, yet which is in Jesse island modeled after I tick island.
Josh Moore: So this is.
Josh Moore: gather town.
yeah.
Deborah Schmidt: I would personally support using the phone for most cases, because you can just read up on it and sync asynchronously and I, for example, like we I told me over to get the last month and I just cannot keep up with all the communication channels at all, it just this so much.
Josh Moore: So that's actually a good point Deborah all right.
Josh Moore: i've struggled with this What could we do an image sc like do we need a new category or a new tag to make people feel comfortable to just.
Josh Moore: Use discourse like it's a chat because I discourse is great, like, I think it works wonderfully but i've had a hard time getting people to feel comfortable just.
Deborah Schmidt: yeah I agree.
Josh Moore: You know, so if someone knows how to fix that barrier i'm all for staying on discourse.
Deborah Schmidt: I thought about that for a while and I think it would be nice to have a better starting page that you could personalize.
Deborah Schmidt: And where you could say, these are the texts that i'm interested in and like kinetic organize them and then maybe see where take then what's unanswered and things like that and tidy looked a bit into it and you can write plugins for this course, but I think we are using.
Deborah Schmidt: I like we don't say first right.
Deborah Schmidt: it's like subliminal paid version, and they are limited, when it comes to writing your own plugins are completely restricted.
Deborah Schmidt: So I think that can show what we have.
Josh Moore: We pay quite a lot and they're very responsive, so if we say we want something there's a developer from discourse who sits in our slot our discourse and response so.
Josh Moore: You know if you yeah so if.
Josh Moore: it's a bit weird to have it be all commercial but on the other hand, it just kind of work so.
Deborah Schmidt: yeah I totally understand that I just from what I read, I read that it's limited when.
Deborah Schmidt: that's not the case that's that could really be an opportunity to.
Deborah Schmidt: make it more person and less and treating like let's.
Deborah Schmidt: Say that people go there and you just have a list of huge topics and then they leave again right.
Josh Moore: So I don't know how, so this is why I created the in gfs group because basically people were saying i'm not seeing what you're saying josh I don't know what's going on, I was like crap you know so it's like.
Josh Moore: We have we've brought our whole community multiple communities together and now, people are lost, and like okay that's bad.
Josh Moore: So, if anyone knows about.
Josh Moore: So if you know.
Deborah Schmidt: yeah I really would like to to to contribute their.
Josh Moore: Thank you kyle So yes, like in send it my way and we'll try to get it installed and then just try it out awesome for support.
Josh Moore: Okay, four minutes last call.
Josh Moore: You still have your whiskey.
one.
Juan Nunez-Iglesias: it's all gone I do need to go down for another.
Josh Moore: was good, seeing everyone.
Josh Moore: Thank you for coming.
To keep.
Josh Moore: you'll see the notes on images see.
Josh Moore: don't be a stranger.
Guillaume Gay: cetera et cetera.
Juan Nunez-Iglesias: So thanks for organizing.
Josh Moore: i'll stick around if anyone wants to say.
Jason Swedlow: Good see well.
Eric Perlman: I was.
Eric Perlman: I was curious how's your durable answer tinkering going.
Josh Moore: Well, I can get it running and all.
Josh Moore: But I can't figure out user interface, so I can get my Czar loaded but it doesn't like the five dimensions are I assume it's wanting a three dimensional is our.
Eric Perlman: room it'll take n dimensional if you click I think I left the link at some point on them it's forum, but the key thing is the Jason I use their for mapping dimension, so it wants it'll take n dimensional, but it really wants to know what X, Y Z and car.
Josh Moore: So I tried my best to teach it what X, Y Z and Z was but it didn't learn So if you could send me the json that would be lovely.
Eric Perlman: Okay yeah the interface is not at all intuitive.
Eric Perlman: It is it's.
Eric Perlman: Totally functional but it's a translation matrix of this dimension maps to this dimension and have you noticed it's totally bizarre.
Josh Moore: But yeah it should it shouldn't so I went for the inverse identity matrix and it.
Josh Moore: didn't work.
Eric Perlman: Well, I ended up needing to do not even the inverse identity matrix they needed.
Eric Perlman: Well okay depends on which state I don't think I what I did for bio formats to rile put, which is what you're probably doing this on.
Eric Perlman: The main one is channel.
Eric Perlman: What you can't do see carrot unless all the channels and trump together right now I did finally create a neuro plantation for that.
Eric Perlman: Because JEREMY JEREMY he's the only one of the universe will ever be able to implement that whereas I would be able to figure out how to at least read the old me tiff or omens our metadata and do something with it.
Josh Moore: find the link for it at this little bit ago yeah so 284 so i'll follow that she went.
Eric Perlman: To see your own posts on the image se forum.
Josh Moore: He certainly with search.
Josh Moore: The search is really good and discourse if you learn all the.
Josh Moore: There are a ton of keywords so i've i've added a couple PRS to discourse it's pretty well done, oh.
Eric Perlman: yeah so i'm going to paste this thread.
Eric Perlman: I had a little link a link in there that says drug lancer DEMO if you click that and then click on the top right corner the braces you can see.
Eric Perlman: You can look at the Jason and, among other things, you could copy and paste roughly where I described the layers or you know.
Eric Perlman: The dimension i'm not sure which part of this.
Josh Moore: dimension because that's empty so layers.
Josh Moore: Is no fillers fillers transform meet.
Eric Perlman: You should be able to have more or less copy and paste that directly in the middle three parts it.
Eric Perlman: it's one thing to be clear about nerd glance or no one far as I can tell, except JEREMY actually ever uses the interface for doing any of this all like if the Sebastian sons lab and everyone else doing things based on neuroscience or.
Eric Perlman: In almost all in Python up to doing Jason and updating the States.
Eric Perlman: Is the main interaction, people are doing with it.
Josh Moore: good to know okay i'll give it to play, thank you.
Eric Perlman: I like the model of the way of dealing with the dimensions and whatnot.
Eric Perlman: yeah do you want most of you have multiple channels and the same chunk it has a cute little feature where you can name it see what the carrot.
Eric Perlman: And then the shaders get that as dimensions zero the end so you can have a shader that combines channel 01 and two and rgb, for example in the word three channel image.
Eric Perlman: I noticed.
Eric Perlman: A lot of activity of the bio formats to raw in the last like week.
Eric Perlman: i'm excited about chug sizes, that I was very happy to see you're mentioning that chunk sizes should extend the things other than X and y.
Josh Moore: yeah I think I mean I think we're well we're focusing on dead so.
Josh Moore: i'm.
Josh Moore: David wood.
Eric Perlman: Right, but what you're generalizing for Z like.
Josh Moore: Well, except it's a bit worse so Z is worse because you have to do the down sampling.
Josh Moore: Or we want to do the down sampling and then and then.
Josh Moore: Changing the chunk size of see should just be kind of are you know super simple.
Josh Moore: I think, David can scream at me if i'm wrong.
David Gault: yeah I mean.
David Gault: The issue with doing the done like chunk size and see is more legacy file formats issues, the elections are issues at the minute.
David Gault: You know, actually implementing started shopping in multiple dimensions isn't.
David Gault: isn't too big, of an issue for.
Eric Perlman: isn't channel basically the outer loop of almost any of the integrators or is it, I guess, time and channel.
Eric Perlman: I guess I didn't I didn't work on data sets with one of the one time went usually so I guess I kind of ignore that.
Eric Perlman: The down sampling, I guess, I didn't could have brought it up you're mentioning multi scales earlier that is it's still like.
Eric Perlman: not clear whether one always one wants to be able to both down sample in just XY plane, or sometimes in xyz planes and so being able to.
Eric Perlman: kind of easily do one or the other sort of matters and the em world generally is down sample in X and y until you get ice a Tropic and then you do all three.
Josh Moore: Interesting okay.
Sebastien Besson: does depend on your volume essentially if you got something which is largely ISO Tropic generally you're doing X, Y Z.
Sebastien Besson: You know, it depends on how Fini essentially how thin your initial structure is essential, even the the whole doubt, I mean wsi word good you're largely to the can be stuck but really you're more to the event anything so while the lead sheet and the emmys here's.
Sebastien Besson: My big block So if I start only doing ex wife and.
Sebastien Besson: I actually don't benefit so much from it down sampling.
Eric Perlman: yeah I think with so that's what said they'll dvm the suit that sorry cereal section em is usually the first couple layers are just X, Y until you get it Tropic ish and then it's maintained, whereas like get them some the whole way you would do it.
Eric Perlman: Anyway, I want to go to bed it's late thanks for having us.
Josh Moore: well.
Sebastien Besson: Are you coming later i'll you see it coming tonight.
Eric Perlman: No, no, I will not, I actually have like.
Eric Perlman: This is the first day of which i've now been have been apple aligned meetings at my schedule at that time.
Eric Perlman: Which is going to be fun to navigate because there's two of them that i'm supposed to absolutely attend so i'm going to do the zoom on one window webex, on the other, and see our associates, and unfortunately I don't think I can add, and you have that on my phone, for good measure.
Josh Moore: You get bonus points, if you show up.
Eric Perlman: My cat may show up how's that.
Josh Moore: Okay that's me, I will take a character.
Eric Perlman: There yeah.
Eric Perlman: Okay i'm good I guys.
tonight.
Juan Nunez-Iglesias: as well.
Josh Moore: All right, take care.
Everyone.
Nicolas Vinuesa: Thank you.
Josh Moore: All right.
Josh Moore: You guys take care.