Ecosyste.ms: Timeline
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pgarrison pushed 3 commits to main AllenCell/benchmarking_representations
pgarrison closed a pull request on AllenCell/benchmarking_representations
Clarify that image_preprocessing is only for punctate structures
Follow-up to address @ritvikvasan's comment on #54 more thoroughly. # Changes * [Install mdformat-gfm-alerts to allow ![NOTE]](https://github.com/AllenCell/benchmarking_representations/commit/0...
pgarrison opened a pull request on AllenCell/benchmarking_representations
Clarify that image_preprocessing is only for punctate structures
# Changes * [Install mdformat-gfm-alerts to allow ![NOTE]](https://github.com/AllenCell/benchmarking_representations/commit/0c73608d6276507e23b232530189b0522f46afdf) in our docs. This required upg...
pgarrison created a branch on AllenCell/benchmarking_representations
preprocessing-docs - Benchmarking different methods for extracting unsupervised representations from images
pgarrison pushed 15 commits to main AllenCell/benchmarking_representations
- Update project tree developer docs for new organization 93fa657
- Split up documentation a18be78
- Clean up arrows 34343b2
- Instruction clarifications including --cores all c9e0a71
- Update location of br folder 7e0bb18
- Update location of br folder 6252883
- image_preprocessing isn't in src/br 2877ff8
- Dataflow diagram 3883d44
- Newline to put image below text 5840886
- Replace image overview with text outline 9766a9d
- Preprocessing instructions know there are two environments 25900aa
- Link to PREPROCESSING.md, not image_preprocessing/README.md 3161629
- Alignment, masking, and registration is only for punctate structures 3f5da87
- Merge remote-tracking branch 'origin/main' into overhaul-readme b67b957
- Merge pull request #54 from AllenCell/overhaul-readme Split README into separate documenation pages d2be7ef
pgarrison closed a pull request on AllenCell/benchmarking_representations
Split README into separate documenation pages
# Issues addressed * README is dense and organization is unclear. We want to write to multiple audiences who want to use this for different purposes. * Docs include paths in tree diagrams that I ...
pgarrison pushed 4 commits to overhaul-readme AllenCell/benchmarking_representations
pgarrison created a review comment on a pull request on AllenCell/benchmarking_representations
Done in [3f5da87](https://github.com/AllenCell/benchmarking_representations/pull/54/commits/3f5da87097e55887e09f27ec81159bf2edc36d09)
pgarrison pushed 1 commit to overhaul-readme AllenCell/benchmarking_representations
- Alignment, masking, and registration is only for punctate structures 3f5da87
pgarrison pushed 2 commits to scripts_features_rebased AllenCell/benchmarking_representations
pgarrison pushed 1 commit to Pre-Commit-analyses AllenCell/benchmarking_representations
- Remove accidentally commited files 8047c10
pgarrison created a review comment on a pull request on AllenCell/benchmarking_representations
FYI the leading underscore convention is that variables named with a leading underscore are internal to the module/class/object they are defined in and not to be used outside of that context. So im...
pgarrison created a review comment on a pull request on AllenCell/benchmarking_representations
This seems non-portable? Doesn't have to be fixed in this PR since we are already tracking this issue #9
pgarrison created a review on a pull request on AllenCell/benchmarking_representations
I didn't test this myself but from the diff it looks good to me. Github doesn't let me approve this PR since I opened it, but this is Ritvik's code -- I just rebased it.
pgarrison created a review on a pull request on AllenCell/benchmarking_representations
I didn't test this myself but from the diff it looks good to me. Github doesn't let me approve this PR since I opened it, but this is Ritvik's code -- I just rebased it.
pgarrison created a review comment on a pull request on AllenCell/benchmarking_representations
Delete this?
pgarrison closed a draft pull request on AllenCell/benchmarking_representations
Move all notebooks to scripts
This PR does a few things 1. Delete notebooks fig2-7 2. Add `run_embeddings` script to compute embeddings e.g. `python src/br/analysis/run_embeddings.py --save_path "./outputs/" --sdf False --...
pgarrison created a comment on a pull request on AllenCell/benchmarking_representations
@ritvikvasan closing this in favor of #58. Please take over that PR
pgarrison pushed 1 commit to overhaul-readme AllenCell/benchmarking_representations
- Link to PREPROCESSING.md, not image_preprocessing/README.md 3161629
pgarrison pushed 1 commit to overhaul-readme AllenCell/benchmarking_representations
- Preprocessing instructions know there are two environments 25900aa
pgarrison opened a draft pull request on AllenCell/benchmarking_representations
Move all notebooks to scripts
This is @ritvikvasan's PR This PR does a few things 1. Delete notebooks fig2-7 2. Add `run_embeddings` script to compute embeddings e.g. `python src/br/analysis/run_embeddings.py --save_pat...
pgarrison created a branch on AllenCell/benchmarking_representations
scripts_features_rebased - Benchmarking different methods for extracting unsupervised representations from images
pgarrison pushed 15 commits to Pre-Commit-analyses AllenCell/benchmarking_representations
- Move image_preprocessing to its own subpackage 749b11e
- Migrate image_preprocessing to pdm 4ba4029
- Install ome-zarr from PyPi, not github 1e664c0
- Install exact versions Ritvik used 7d0fff8
- Remove extra dependencies c7cdc17
- Add rudimentary instructions for preprocessing 2abae85
- Lock file has Ritvik's version of setuptools bd0cbb9
- Preprocessing instructions include cd 472ee5b
- Remove boilerplate docs 432fd08
- Merge pull request #42 from AllenCell/preprocessing-separate-venv Preprocessing installation (not usage) instructions 68f2e81
- Merge pull request #45 from AllenCell/remove-docs-boilerplate Remove boilerplate docs 30528fa
- Merge pull request #44 from AllenCell/csv_logger add csv logger to all experiments 7164e8c
- Remove extraneous backtick 65a139f
- Merge pull request #53 from AllenCell/image-preprocessing-instructions-typo Remove extraneous backtick 05a55fd
- run pre-commit 4523efd
pgarrison pushed 1 commit to overhaul-readme AllenCell/benchmarking_representations
- Preprocessing instructions know there are two environments 396a749