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Pycytominer training - #7060
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Pycytominer training#7060
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rmassei
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dianichj and
kostrykin
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September 2, 2026 07:49
d33bs
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Sep 10, 2026
axiomcura
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Sep 20, 2026
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Really cool, thanks for developing this! I left some comments. Please feel free to ping me if you have any questions c:
Awesome work, kudos!
Co-authored-by: Dave Bunten <ekgto445@gmail.com>
Co-authored-by: Erik Serrano <31600622+axiomcura@users.noreply.github.com>
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Thanks a lot @d33bs and @axiomcura for your comments are reviews! |
dianichj
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Awesome tutorial and great work! Very easy to follow. Here is my round of comments and suggestions.
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| We have now a table with just 4 lines, collapsed in the selected unique conditions! | ||
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| > <hands-on-title> Extract Pycytominer workflow from history </hands-on-title> | ||
| > 1. Now we can extract the workflow for batch processing: | ||
| > - Name it "pycytominer-full-steps". |
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{% snippet faqs/galaxy/workflows_extract_from_history.md %}
I would suggest to add the snippet here, right below item 1, and then the naming part.
| > <hands-on-title> Extract Pycytominer workflow from history </hands-on-title> | ||
| > 1. Now we can extract the workflow for batch processing: | ||
| > - Name it "pycytominer-full-steps". | ||
| > - Don't treat `01_platemap.tsv` and `01_single_cells.tsv` as inputs (the workflow is supposed to be applied to the image-based profiles directly). |
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This step has been confusing in other tutorials. So based on the interface we can say "uncheck."
dianichj
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Awesome tutorial and great work! Very easy to follow. Here is my round of comments and suggestions.
Co-authored-by: Diana Chiang Jurado <122611454+dianichj@users.noreply.github.com>
dianichj
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beatrizserrano
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This PR adds a new hands-on tutorial to show how to use Pycytominer tool suite in Galaxy
File location: topics/imaging/tutorials/pycitominer/workflows/test-data
What this tutorial covers
closes FAIR-imaging/galaxy-image-community#76