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hammerlab / cytokit

Microscopy Image Cytometry Toolkit
Apache License 2.0
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Make example data sets public #9

Open armish opened 6 years ago

armish commented 6 years ago

Here are the ones that we are familiar with and trust the most:

$ gsutil ls gs://musc-codex/datasets/ \
     | grep "20180706\|20180614" \
     | xargs -I@ -P1 bash -c "gsutil du -sh @"

6.65 GiB    gs://musc-codex/datasets/20180614_D22_RepA_Tcell_CD4-CD8-DAPI_5by5
9.88 GiB    gs://musc-codex/datasets/20180614_D22_RepB_Tcell_CD4-CD8-DAPI_5by5
9.4 GiB     gs://musc-codex/datasets/20180614_D23_RepA_Tcell_CD4-CD8-DAPI_5by5
8.81 GiB    gs://musc-codex/datasets/20180614_D23_RepB_Tcell_CD4-CD8-DAPI_5by5
5.55 GiB    gs://musc-codex/datasets/20180706-Donor22-R2-Tcell-CODEX_CD3CD4CD85BY5
5.38 GiB    gs://musc-codex/datasets/20180706-Donor23-R2-Tcell-CODEX_CD3CD4CD85BY5

These would also make testing the framework easier for everybody. The only thing we have to make sure is that making these data sets won't be that costly. We can go with a service like figshare but not sure how their downloading bandwidth scales if we need to download it over and over again.

@hammer: any suggestions?

hammer commented 6 years ago

Those are a bit large for Google Drive.

Nature recommends the IDR: cf. their submission guidelines.

If IDR doesn't want our images, maybe Dryad? I dunno. We should ask Anne Carpenter.

hammer commented 6 years ago

The Cell Image Library is another alternative

armish commented 5 years ago

We now have a dedicated public bucket: gs://cytokit. Added data sets that are relevant to the manuscript:

$ gsutil ls gs://cytokit/datasets/*
gs://cytokit/datasets/cellsize/:
gs://cytokit/datasets/cellsize/20181024-d38-act-20X-5by5/
gs://cytokit/datasets/cellsize/20181024-d38-unstim-20X-5by5/
gs://cytokit/datasets/cellsize/20181024-d39-act-20x-5by5/
gs://cytokit/datasets/cellsize/20181024-d39-unstim-20x-5by5/
gs://cytokit/datasets/cellsize/20181024-jurkat-20X-5by5/
gs://cytokit/datasets/cellsize/20181024-jurkat2-20X-5by5/
gs://cytokit/datasets/cellsize/20181026-pmel-act-20x-5by5/
gs://cytokit/datasets/cellsize/20181026-pmel-act-60x-1by1/
gs://cytokit/datasets/cellsize/20181026-pmel-act-60x-5b5/
gs://cytokit/datasets/cellsize/20181026-pmel-us-20x-5by5/
gs://cytokit/datasets/cellsize/20181026-pmel-us-60x-1by1/

gs://cytokit/datasets/cellular-marker/:
gs://cytokit/datasets/cellular-marker/20180614_D22_RepA_Tcell_CD4-CD8-DAPI_5by5/
gs://cytokit/datasets/cellular-marker/20180614_D22_RepB_Tcell_CD4-CD8-DAPI_5by5/
gs://cytokit/datasets/cellular-marker/20180614_D23_RepA_Tcell_CD4-CD8-DAPI_5by5/
gs://cytokit/datasets/cellular-marker/20180614_D23_RepB_Tcell_CD4-CD8-DAPI_5by5/
gs://cytokit/datasets/cellular-marker/20180927-Tcell-CD3_CD4_CD8_DAPI-20X-5by5/

Will add pointers from the README before closing this issue.