Include atlas information in annotation file

[jcfr]

What's the problem this feature will solve?

Annotation saved using CellLocator do not include reference to the associated atlas. Without the context, interpreting the saved annotation is not possible.

Describe the solution you'd like

Overview

Update the file format to include atlas details like the type, version, resolution, ...

At a high level, we could consider:

• (a) saving atlas type and cell-locator software version. Knowing the software version would allow to retrieve the relevant details by inspecting the source code.

• (b) explicitly saving all details.

I suggest we go with (b).

Suggested information for CCF

"atlas": {
    "type": "ccf",
    "average_template": {
        "version": "2009",
        "resolution": 50,
        "url": "http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/average_template/average_template_50.nrrd",
        "checksum": "sha256:6114c341d526f9782ca93b314b3244bb0c4c6cea17045f432d4cda63339915aa"
    },
    "annotation": {
        "version": "2017",
        "url": "http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2017/annotation_50.nrrd",
        "checksum": "sha256:84e7cecea1b03af16e923c3639602b8324929f833425ba03582bf56f962ea0d4"
    }
}

Suggested information for MNI

"atlas": {
    "type": "mni",
    "average_template": {
        "version": "2009",
        "type":  "mni_icbm152_nlin_sym_09b_nifti",
        "resolution": 50,
        "url": "http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_sym_09b_nifti.zip",
        "checksum": "sha256:acce3b85039176aaf7de2c3169272551ddfcae5d9a4e5ce642025b795f9f1d20"
    },
    "annotation": {
        "version": "2020.1",
        "url": "http://download.alleninstitute.org/informatics-archive/allen_human_reference_atlas_3d_2020/version_1/annotation_full.nii.gz",
        "checksum": "sha256:2b05581e39c44f2623d9b0a69f64e3df0823c20d054abef92973812313335dc3"
    }
}

Alternative Solutions

Recommend an annotation file naming scheme.

Additional context

NA

[jcfr]

Waiting we discuss the details with the team , I suggest we go with the following:

"atlas": {
  "type: "ccf"
}

or

"atlas": {
  "type: "mni"
}