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Examples for Microscopy BEP031 #286

Merged
merged 49 commits into from
Jan 12, 2022
Merged

Examples for Microscopy BEP031 #286

merged 49 commits into from
Jan 12, 2022

Commits on Aug 3, 2021

  1. Added two first microscopy example datasets, OME-TIFF and PNG files.

    @etiennebergeron
    etiennebergeron committed Aug 3, 2021
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  2. Modified the datasets to make 'sem001' without sample files and 'sem0… 

    …02' with sample files.
    @etiennebergeron
    etiennebergeron committed Aug 3, 2021
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Commits on Aug 6, 2021

  1. Renamed with uppercase suffixes and removed couple of recommended JSO… 

    …N fields in the 'sem002' subject's file sidecar.
    @etiennebergeron
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  2. Rename sub-01_sem.json to sub-01_SEM.json

    @etiennebergeron
    etiennebergeron authored Aug 6, 2021
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  3. Rename sub-01_sample-A_sem.json to sub-01_sample-A_SEM.json

    @etiennebergeron
    etiennebergeron authored Aug 6, 2021
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  4. Rename sub-01_sample-A_sem.png to sub-01_sample-A_SEM.png

    @etiennebergeron
    etiennebergeron authored Aug 6, 2021
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Commits on Aug 9, 2021

  1. As discussed with MH, every microscopy datasets need the entity 'samp… 

    …le'. Added it to the 'sem001' dataset and incorporated the session folder structure for 'sem002'.
    @etiennebergeron
    etiennebergeron committed Aug 9, 2021
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Commits on Aug 12, 2021

  1. Modified OMETIFF's metadata and its JSON file to fit the OME required… 

    … fields 'PhysicalSizeX', Y and Z.
    @etiennebergeron
    etiennebergeron committed Aug 12, 2021
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  2. Changed back 'PixelSizeUnits' to um in the JSON, was left to 'nm' aft… 

    …er some tests.
    @etiennebergeron
    etiennebergeron committed Aug 12, 2021
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Commits on Aug 19, 2021

  1. Updated the example datasets; added 'microscopy' in the folder name, … 

    …added multiple samples per subject and removed the column 'derived_from' in samples.tsv.
    @etiennebergeron
    etiennebergeron committed Aug 19, 2021
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Commits on Sep 8, 2021

  1. Update microscopy_SPIM001/dataset_description.json 

    Co-authored-by: mariehbourget <[email protected]>
    @etiennebergeron @mariehbourget
    etiennebergeron and mariehbourget authored Sep 8, 2021
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  2. Update microscopy_SEM001/README 

    Co-authored-by: mariehbourget <[email protected]>
    @etiennebergeron @mariehbourget
    etiennebergeron and mariehbourget authored Sep 8, 2021
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  3. Update microscopy_SPIM001/README 

    Co-authored-by: mariehbourget <[email protected]>
    @etiennebergeron @mariehbourget
    etiennebergeron and mariehbourget authored Sep 8, 2021
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  4. Update microscopy_SPIM001/dataset_description.json 

    Co-authored-by: mariehbourget <[email protected]>
    @etiennebergeron @mariehbourget
    etiennebergeron and mariehbourget authored Sep 8, 2021
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  5. Update microscopy_SEM001/dataset_description.json 

    Co-authored-by: mariehbourget <[email protected]>
    @etiennebergeron @mariehbourget
    etiennebergeron and mariehbourget authored Sep 8, 2021
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  6. Removed BEP version

    @etiennebergeron
    etiennebergeron committed Sep 8, 2021
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  7. Removed BEP version in JSON files

    @etiennebergeron
    etiennebergeron committed Sep 8, 2021
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  8. Replace MIT for CC0 license.

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  9. Replace MIT License for CC0.

    @etiennebergeron
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  10. Replace MIT License for CC0.

    @etiennebergeron
    etiennebergeron committed Sep 8, 2021
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  11. Updated example datasets based on MH recommendations (chunk entity fo… 

    …r SPIM dataset, snd session for SEM dataset, etc.).
    @etiennebergeron
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  12. Removed LICENSE files from SEM and SPIM datasets.

    @etiennebergeron
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  13. Update microscopy_SEM001/README 

    Co-authored-by: mariehbourget <[email protected]>
    @etiennebergeron @mariehbourget
    etiennebergeron and mariehbourget authored Sep 8, 2021
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  14. Update microscopy_SPIM001/sub-01/microscopy/sub-01_sample-A_SPIM.json 

    Co-authored-by: mariehbourget <[email protected]>
    @etiennebergeron @mariehbourget
    etiennebergeron and mariehbourget authored Sep 8, 2021
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  15. Update microscopy_SPIM001/sub-01/microscopy/sub-01_sample-B_SPIM.json 

    Co-authored-by: mariehbourget <[email protected]>
    @etiennebergeron @mariehbourget
    etiennebergeron and mariehbourget authored Sep 8, 2021
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  16. Update microscopy_SPIM001/README 

    Co-authored-by: mariehbourget <[email protected]>
    @etiennebergeron @mariehbourget
    etiennebergeron and mariehbourget authored Sep 8, 2021
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  17. Edited the SPIM Manufacturer/Model and added the stain entity+SampleS… 

    …taining field.
    @etiennebergeron
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Commits on Sep 16, 2021

  1. Update microscopy_SPIM001/README 

    Co-authored-by: mariehbourget <[email protected]>
    @etiennebergeron @mariehbourget
    etiennebergeron and mariehbourget authored Sep 16, 2021
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  2. Update microscopy_SEM001/dataset_description.json 

    Co-authored-by: mariehbourget <[email protected]>
    @etiennebergeron @mariehbourget
    etiennebergeron and mariehbourget authored Sep 16, 2021
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  3. Update microscopy_SPIM001/dataset_description.json 

    Co-authored-by: mariehbourget <[email protected]>
    @etiennebergeron @mariehbourget
    etiennebergeron and mariehbourget authored Sep 16, 2021
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  4. Empty OME-TIFF's metadata update

    @etiennebergeron
    etiennebergeron committed Sep 16, 2021
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  5. Merge branch 'bids-standard:master' into bep031

    @mariehbourget
    mariehbourget authored Sep 16, 2021
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Commits on Sep 28, 2021

  1. Entities order modified; <chunk> at the end. Only affects the 'SPIM' … 

    …dataset.
    @etiennebergeron
    etiennebergeron committed Sep 28, 2021
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Commits on Oct 16, 2021

  1. Metadata fields changes; 'ShrinkageFactor' now 'TissueDeformationScal… 

    …ing' and 'Environment' now 'SampleEnvironment'.
    @etiennebergeron
    etiennebergeron committed Oct 16, 2021
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Commits on Oct 19, 2021

  1. Since 'ShrinkageFactor' became 'TissueDeformationScaling', the values… 

    … (in %) have been changed from 2 to 98.
    @etiennebergeron
    etiennebergeron committed Oct 19, 2021
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Commits on Nov 4, 2021

  1. Update microscopy_SEM001/sub-01/sub-01_sessions.json 

    Co-authored-by: Julia Guiomar Niso Galán <[email protected]>
    @mariehbourget @guiomar
    mariehbourget and guiomar authored Nov 4, 2021
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  2. Merge branch 'bids-standard:master' into bep031

    @mariehbourget
    mariehbourget authored Nov 4, 2021
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Commits on Dec 4, 2021

  1. 1. Add one json file per chunk and the ChunkTransformationMatrix and … 

    …ChunkTransformationAxis field.

2. Add an explanation in the README of the dataset.
    @konantian
    konantian committed Dec 4, 2021
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  2. Code clean

    @konantian
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  3. Add space to values in "SampleEnvironment" field

    @konantian
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  4. Merge pull request #2 from neuropoly/add-json-per-chunk 

    Add json per chunk
    @konantian
    konantian authored Dec 4, 2021
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  5. 1. Change the data_type "microscopy" to "micr" 

    2. Change "BIDSVersion" of example datasets to "1.7.0"
    @konantian
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Commits on Dec 5, 2021

  1. Add space to values in the "SampleEnvironment" field to fit the new r… 

    …equirements.
    @konantian
    konantian committed Dec 5, 2021
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  2. Merge pull request #3 from neuropoly/update-data-type-and-bids-version 

    Update the data type and BIDSVersion
    @konantian
    konantian authored Dec 5, 2021
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Commits on Dec 6, 2021

  1. Merge branch 'bids-standard:master' into bep031

    @mariehbourget
    mariehbourget authored Dec 6, 2021
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  2. Rename datasets to micr_SEM and micr_SPIM

    @mariehbourget
    mariehbourget committed Dec 6, 2021
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  3. Add a microscopy summary table to the README.md

    @mariehbourget
    mariehbourget committed Dec 6, 2021
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Commits on Dec 9, 2021

  1. Add jcohenadad as maintainer of the examples

    @mariehbourget
    mariehbourget committed Dec 9, 2021
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Commits on Dec 10, 2021

  1. Corrections to the OME-XML structure according to the OME schema docu… 

    …mentation.
    @etiennebergeron
    etiennebergeron committed Dec 10, 2021
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