Issue on page /machine_learning.html

[jasperhyp]

The path cpg0016-jump/SOURCE/workspace/segmentation/cellpose/objects/BATCH/ for cpg0016-jump (specified on page) does not exist in the AWS S3 bucket.

[ErinWeisbart]

They have been uploaded for source_8 and the uploads for other sources are in progress.
(Granular details are available in #73 though I will note in this issue as well when all of the uploads have completed)
Thanks for your patience.

[jasperhyp]

Thank you for the clarification, Erin! I went into source_8 and was able to identify single cell images in e.g. https://open.quiltdata.com/b/cellpainting-gallery/tree/cpg0016-jump/source_8/workspace/segmentation/cellpose_202404/objects/J1/A1170384/A1170384.zarr/source_8__J1__A1170384__A01__3/single_cell_data/. However, it seems the file is in a different format compared with those in e.g. cpg0019-moshkov-deepprofiler/broad/training_images/BBBC036/, which is typically a 960x160 TIFF image displaying 6 channels and then a segmentation mask. Could you please point me to potential documentations as well? Thanks in advance!

[ErinWeisbart]

The cpg0019 files are described in Moshkov et al 2024 https://www.nature.com/articles/s41467-024-45999-1

The cpg0016 files have not yet been described in a publication but the workflow being used to create the image crops is here https://github.com/theislab/jump-cpg0016-segmentation