https://github.com/sbesson/embrc0001

Template repository for annotating EMBRC images
https://github.com/sbesson/embrc0001

Last synced: about 1 month ago
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Template repository for annotating EMBRC images

• Host: GitHub
• URL: https://github.com/sbesson/embrc0001
• Owner: sbesson
• Created: 2018-08-28T12:19:37.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2018-10-05T20:38:51.000Z (about 6 years ago)
• Last Synced: 2023-10-20T22:59:07.982Z (about 1 year ago)
• Homepage:
• Size: 10.7 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
## Prerequisites

Create a Python virtual environment and install the prerequisites from the

[requirements](requirements.txt) file:

    virtualenv /tmp/venv

    /tmp/venv/bin/pip install -r requirements.txt

Download OMERO.py from the [OMERO downloads](https://www.openmicroscopy.org/omero/downloads/) and extract it.

Activate the virtual environment, and check the `metadata` command is

registered by the command-line interface shipped with OMERO.py:

    /tmp/venv/bin/activate

    cd /path/to/OMERO.py

    bin/omero metadata -h

## Annotating images

The image annotation is done in three steps:

-   first an CSV file needs to be created containing the annotations.

-   then the CSV file is converted into an OMERO.table attached to the

    top-level Project. 

-   finally the OMERO.table can be converted into a series of map annotations

    for each image.

### Annotation file

This file can have as many columns as desired. For images in a Project/Dataset/Hierarchy, each row correspond to an image and two columns `Dataset Name` and `Image Name` are required to find the image.

### Bulk annotations

First create an OMERO.table (`bulk_annotations`) attached the top-level project from the [annotation.csv](annotation.csv) file:

    bin/omero metadata populate --file annotation.csv Project:

With OMERO 5.4.8, each row of this table should be viewable in the Web client

by expanding the Tables tab on the right-hand panel of each image.

### Map annotations

This conversion is done by a [configuration file](bulkmap.yml) which describes which columns should be turned into key/value pairs and whether some columns should be grouped together using a namespace e.g. Organism.

Run the `metadata populate` command with the `bulkmap` context:

    bin/omero metadata populate --context bulkmap --cfg bulkmap.yml Project:

This should create map annotations for each image that can be viewed in the

right-hand panel of the web client. Some of these annotations will have

namespaces allowing them to be searchable using the

[OMERO.mapr](https://github.com/ome/omero-mapr) web app.