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base repository: mehta-lab/VisCy
base: v0.2.0
head repository: mehta-lab/VisCy
compare: v0.2.1
- 7 commits
- 44 files changed
- 8 contributors
Commits on Aug 8, 2024
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version lighting CLI example (#128)
* version lighting CLI example * add some documentation * ignore slurm output * add more tips
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Commits on Aug 9, 2024
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Updated code (contrastive learning) (#130)
* updated prediction code to test specific cells * updated kernel and stride * updated kernel and stride * new training script and predict takes in output path as parameter * passing ci requirements * fixed error for output path * fixed error for output path * fixed formatting * format resolved * docstrings for methods that parse tracks --------- Co-authored-by: Shalin Mehta <shalin.mehta@czbiohub.org>
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Configurable drop path rate in contrastive models (#131)
* log instead of print * configurable drop path rate * fix docstring
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Commits on Aug 14, 2024
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Config-based prediction with Xarray-based output format (#132)
* use callback to write prediction embeddings * moving over the script to compute infection score from contrastive_update * delete unused stem module * organize scripts and CLIs for contrastive phenotyping * add dependencies for prediction * export embedding dataset reader function * add more plots to script * use real paths in predict config * do not require seaborn and umap-learn for base install * use relative path in example job script * add docstrings for embedding writer and reader * don't assign unused grid object * show time and id as hover data in interactive plot * fix typo * fix script to test data i/o * ignore accidental lightning_logs * add plotly and nbformat to visual dependencies * tweak predict cli example * add another plot type - raw features of random samples * comment on speed of clustermap * add prediction config example to specify log path * simplify env var in job script and match cpu count with config * vectorize string concatenation --------- Co-authored-by: Shalin Mehta <shalin.mehta@czbiohub.org>
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Commits on Aug 17, 2024
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Plot tracks in latent space and real space (#135)
* slice by FOV and track * proper indexing Co-authored-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com> * plot features of a single track * rename (dataset -> embedding_dataset) * trying to read patches of a track * display cells from the chosen track in napari * project a track on umap computed from all features * Animated latent space (#137) * animated latent space * delete duplicate umap calculation --------- Co-authored-by: Shalin Mehta <shalin.mehta@czbiohub.org> * PCA of features and projections --------- Co-authored-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>
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Commits on Aug 31, 2024
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Fix deprecated custom forward method (#151)
* fix deprecated custom forward method * specify device type
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Commits on Sep 6, 2024
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updating the notebook after running it at DLMBL2024 (#149)
* updating the notebook after running it at DLMBL2024 Co-authored-by: Diane Adjavon <diane.adjavon@icloud.com> Co-authored-by: AlbertDominguez <albert.dominguezmantes@epfl.ch> Co-authored-by: Anna Foix <afoix@ebi.ac.uk> * adding template for the phase contrast demo * adding custom viscy["examples"] installation * updating the DLMBL2024 exercise and solution ipynb * updating image2image example * adding nbconvert and updating ipynb img2img example * fixing the img2img outline * update structure and links of main README * updating readme links for the pngs * - removing the 'redundant' readme.md - adding the phase contrast example - saving the PhC notebook with images * update setup.sh to handle 0.2 versions only * collapse citations, ignore slurm * clean up citations * addressing Ziwen's comments * cleanup the img2img notebook after testing * updating the inference demo scripts * - making absolute paths on root readme. - description on docstrings for inference demo scripts --------- Co-authored-by: Diane Adjavon <diane.adjavon@icloud.com> Co-authored-by: AlbertDominguez <albert.dominguezmantes@epfl.ch> Co-authored-by: Anna Foix <afoix@ebi.ac.uk> Co-authored-by: Shalin Mehta <2934183+mattersoflight@users.noreply.github.com> Co-authored-by: Shalin Mehta <shalin.mehta@czbiohub.org>
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