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hubmapconsortium / codex-pipeline

CODEX data processing code
GNU General Public License v3.0
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tutorial to follow #26

Open sailseem opened 2 years ago

sailseem commented 2 years ago

Dear developer,

Is there any tutorials to follow to run this codex-based imaging pipeline? Thanks!

VasylVaskivskyi commented 2 years ago

Hi @sailseem , sorry I didn't notice your open issue. We are currently reworking some parts of the pipeline as well as stadardizing the input metadata and data structure. These changes should simplify usage of the pipeline. The new version of the pipeline should be release some time in May. After that we can make a tutorial with a small dataset. If you really need to use the pipeline right now, the best thing would be to organize the data and metadata according to what is described in the README file and metadata_examples folder.