OME Metadata Workshops

Outline

The Data journey
Data/Metadata from IDR
Import options: Demo...

Data workshops

Import Data
Raw Data Analysis
Handle Metadata

Materials available at

https://downloads.openmicroscopy.org/presentations/2018/Users-Meeting/Workshops/Metadata-*

Today's focus: Data from paper

Subdiffraction imaging of centrosomes reveals higher-order organizational features of pericentriolar material

Steffen Lawo, Monica Hasegan, Gagan D. Gupta & Laurence Pelletier

Nature Cell Biology volume 14, pages 1148–1158 (2012)

Code name: idr0021

Preparation: Download from IDR

Docker image using Aspera to acquire data (size 300 MB):

docker run --rm -v /tmp:/data imagedata/download idr0021 . /data/

Import scenarii covered during Demo...

Desktop Client
CLI:
- In-place Import
- Bulk Import

Import Reminder...

ManagedRepository

For Demo, user importing is...

A Facility Manager: importer1 i.e. an OMERO user with some restricted admin privileges
who has Write access to the ManagedRepository

In-place import: symlink


                        $ bin/omero import path/to/image --transfer=ln_s

Bulk Import CLI

Two files are required to describe an import

How to import: bulk.yml


continue: "true"
transfer: "ln_s"
checksum_algorithm: "File-Size-64"
logprefix: "logs/"
output: "yaml"
path: "idr0021.tsv"
columns:
    - target
    - path

What to import: idr0021.tsv


Dataset:name:CDK5RAP2-C /OMERO/in-place-import/idr0021-lawo-pericentriolarmaterial/Raw-files/CDK5RAP2-C/Centrin_PCNT_Cep215_20110506/Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ.dv
Dataset:name:CDK5RAP2-C /OMERO/in-place-import/idr0021-lawo-pericentriolarmaterial/Raw-files/CDK5RAP2-C/Centrin_PCNT_Cep215_20110506/Centrin_PCNT_Cep215_20110506_Fri-1559_0_SIR_PRJ.dv
...

Post Import Data Manipulation: Demo...

CLI: Render data

How to render: renderingdef.yml & renderingdef2.yml


# Specification of rendering settings

channels:
  1:
    # red
    color: "FF0000"
    label: "CEP192-M"
    min: 30
    max: 255
  2:
    # blue
    color: "0000FF"
    label: "CENT2"
    min: 45
    max: 5000

What to render: renderingMapping.tsv


CDK5RAP2-C_     renderingdef.yml
CENT2_  renderingdef2.yml
CEP120/20111106_        renderingdef.yml
CEP120/20111209_        renderingdef2.yml
...