00:21:26 Sebastien Besson: I’ll give reminders at 50 seconds of introduction 00:22:42 Sebastien Besson: 1min 00:23:28 Josh Moore: Dave M. up next. 00:24:11 Robert Haase: I suffer with you Tischi :D 00:24:34 Josh Moore: Then David 00:24:39 Josh Moore: (Pinto) 00:25:20 Josh Moore: Egor next. 00:25:53 Josh Moore: Then Emil. 00:26:22 Josh Moore: Then Eric. 00:26:52 Josh Moore: Then Erin. 00:27:42 Josh Moore: Jean-Karim next. 00:28:42 Josh Moore: Then Juan. 00:29:19 Sebastien Besson: 55s Jean-Karim 00:29:29 Sebastien Besson: Perfect! 1min 00:29:41 Josh Moore: Then Laurent 00:30:22 Josh Moore: Then Raphael 00:30:52 Josh Moore: Then Robert 00:31:27 Josh Moore: Then Stephan 00:32:03 Jason Swedlow: New T-shirt: Big Image Data Cloud Something... 00:32:17 Josh Moore: Warning: moving to the OME team but we can keep it shorter I assume. 00:32:23 Juan Nunez-Iglesias: I would buy that 00:33:09 Josh Moore: David / Frances / J-m / Petr / Seb / Simon / Will 00:35:23 Josh Moore: Oliver 1 minute intro after Will? 00:38:10 Stephan Wagner-Conrad: "ZARR in a nutshell" video would be actually nice 00:39:10 Simon Li: We have a few Jupyter notebooks that introduce Zarr, I'll see if I can find one (the links in the hack.md are examples of using Zarr, but we should have an intro one too) 00:39:11 David Pinto: the demo at OME2020 was very nice and clear 00:39:25 Stephan Wagner-Conrad: agree 00:55:39 jean-marie burel: @simon: https://github.com/ome/omero-guide-python/blob/master/notebooks/zarr-public-s3-multiscale.ipynb 00:55:45 jean-marie burel: I will add it to the doc 00:57:23 Sebastien Besson: http://www.geoapi.org/3.0/javadoc/org/opengis/referencing/doc-files/WKT.html 01:01:16 Sebastien Besson: http://www.neuronland.net/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html right? 01:01:35 David Pinto: does WKT extends to 3D? 01:01:45 Emil Rozbicki: Yes to 3D. 01:10:13 Jason Swedlow: a lot of the segmentations we are working with are Golgi, Actin filopodia. Agree with Josh re: Virginie's work on splines. 01:10:53 Christian Tischer: “Cloud = Someone else’s computer” I like it :) 01:16:07 Christian Tischer: Are there readers and writers for ome.zarr in Java? 01:18:53 Simon Li: @christian David Gault is working on it, he can probably say more on where it's at 01:20:24 Christian Tischer: Would be great in order to get the Fiji/ImageJ community involved into this project. 01:24:18 Josh Moore: YES! 01:24:31 jean-marie burel: FBI: French Bio Imaging :-) 01:24:42 jean-marie burel: not the other one 01:26:10 Jason Swedlow: Probably worth emphasizing that at least at the file format level, we don't intend any of this to be OMERO-specific. 01:26:14 David Pinto: having to upgrade from one ome zarr version to another, seems very similar to change the data from one file format to another and researchers have a "fetish" on the raw data 01:26:30 Josh Moore: After Eric, Jason then David Pinto. 01:26:43 jean-marie burel: @christian: we have example using Imagej-Python (entering via “the back door) and zarr 01:27:18 jean-marie burel: but agree we need to get community involved 01:32:44 Sebastien Besson: Stability + tooling Stephan ? 01:32:58 Sebastien Besson: Are these the main blockers? 01:37:02 Josh Moore: ALL: anyone else have comments/questions on the “cloud” discussion? Otherwise shall we start migrating to “other data types”? 01:37:55 Guillaume Gay: https://github.com/xtensor-stack/xtensor-zarr 01:38:09 Stephan Wagner-Conrad: thank you 01:39:32 David Pinto: yeah, where does one start to create zarr files if they have a bunch of acquisition metadata and just got the binary from the camera? 01:40:21 Simon Li: At the moment? probably bioformats2raw 01:40:50 Eric Perlman: My workflow currently is using bf2raw on a bunch of ndpi files 01:41:01 Will Moore: Or if it’s in OMERO, we’ve been using https://github.com/ome/omero-cli-zarr 01:41:07 David Pinto: isn't bioformats2raw for when you start with a file? 01:42:14 David Pinto: just read the data from the camera, there's no file yet 01:42:28 Stephan Wagner-Conrad: Sebastian: company Internally funding might be one of the most important topics to consider here and bringing the support for the format to the right level in our internal platform 01:43:31 Sebastien Besson: Cheers Stephan 01:45:11 Sebastien Besson: X,y,z,t + features 01:45:41 David Pinto: +precision of localisation 01:46:38 David Pinto: OTFs (complex data type) 01:47:29 Jason Swedlow: @Stephan-- if it is useful, let us know how we can support that effort. 01:47:35 Guillaume Gay: one can thing of spectral images? 01:49:07 David Pinto: proteomics, where the "image data" is a mass spec for each point 01:49:42 David Pinto: or "pixel" 01:50:16 David Pinto: there, your "image" may not even be rectangular 01:51:36 Jason Swedlow: @David We've had several discussions about that. in each case, the producer has been happy to provide a peak list at each pixel, which then is a multi-channel image. Several groups are making those transforms into OME-TIFF. 01:54:39 Sebastien Besson: Plate for example is 100% optional! 01:54:50 Sebastien Besson: _if_ you want a plate you must implement.... 01:55:49 Jason Swedlow: TMAs.... 01:56:04 Josh Moore: I *always* read "TMI" 01:56:21 Sebastien Besson: Yes TMAs to :) 01:58:06 Josh Moore: https://zarr.readthedocs.io/en/v2.5.0/tutorial.html?highlight=lz4#compressors 01:59:58 Jean-Karim Heriche: Some work on compression from EMBL: https://www.biorxiv.org/content/10.1101/164624v1 02:03:46 Egor Panfilov: Thank you for insights! I have to go. 02:05:18 David Pinto: what's the plan for the afternoon meeting? Does it cover different topics (there were binary/metadata on the original proposal) 02:05:30 David Pinto: evening (not afternoon) 02:05:30 Josh Moore: That remains to be seen ;) 02:05:37 Josh Moore: Based on who shows up. 02:10:23 Christian Tischer: Agree with JK 02:11:09 Sebastien Besson: @ngff 02:14:34 Dave Mellert: Hey everyone, I have to run! This was great, thanks for organizing 02:15:17 Christian Tischer: Thanks! Was great! 02:15:18 David Pinto: thank you for setting this up 02:15:24 Raphael Maree: THanks, bye !