Initial release of pycytominer

[gwaybio]

Pycytominer release v0.1

Pycytominer is a python package that implements functions for every step of the image-based profiling pipeline.

Processing image-based readouts of cell morphology, we can now:

• aggregate single cells to form bulk profiles
• subsample single cells to form pseudo bulk replicates
• normalize both single cells and bulk profiles
• apply feature selection functions to remove uninformative morphology features
• generate consensus signatures from replicates

The package currently has 98% test coverage and is fully documented with some examples. We hope that you enjoy using pycytominer, and please report bugs, make recommendations, and discuss any ideas you might have.

What's Changed

• Adding Initial Functions by @gwaygenomics in Adding Initial Functions #1
• Update LICENSE file by @gwaygenomics in Update LICENSE file #2
• Adding Travis yml by @gwaygenomics in Adding Travis yml #3
• Add normalize function by @gwaygenomics in Add normalize function #4
• Adding setup.py by @gwaygenomics in Adding setup.py #7
• Add Cytominer Authors to Setup by @gwaygenomics in Add Cytominer Authors to Setup #8
• Add Covariance Functions by @gwaygenomics in Add Covariance Functions #9
• Adding sparse random projection by @gwaygenomics in Adding sparse random projection #10
• Adding Whitening Transform Method by @gwaygenomics in Adding Whitening Transform Method #13
• Adding feature_select.py function by @gwaygenomics in Adding feature_select.py function #15
• Adding Feature Select Testing by @gwaygenomics in Adding Feature Select Testing #17
• Updating aggregate to work with sqlite files by @gwaygenomics in Updating aggregate to work with sqlite files #16
• Adding random state set function in aggregate.py by @gwaygenomics in Adding random state set function in aggregate.py #18
• Add sqlalchemy to setup.py by @gwaygenomics in Add sqlalchemy to setup.py #19
• Adding codecov to travis by @gwaygenomics in Adding codecov to travis #20
• Adding annotate.py by @gwaygenomics in Adding annotate.py #21
• Updating normalize.py by @gwaygenomics in Updating normalize.py #23
• Updating feature_select.py by @gwaygenomics in Updating feature_select.py #24
• Inferring Features in feature_select.py by @gwaygenomics in Inferring Features in feature_select.py #27
• Add Audit by @gwaygenomics in Add Audit #33
• Try to coerce string input for subsample_n by @gwaygenomics in Try to coerce string input for subsample_n #34
• [hotfix] save quantile in audit by @gwaygenomics in [hotfix] save quantile in audit #35
• [hotfix] make sure to enable audit output! by @gwaygenomics in [hotfix] make sure to enable audit output! #36
• Adding option to compress output data by @gwaygenomics in Adding option to compress output data #40
• Blacklist features by @gwaygenomics in Blacklist features #41
• Inferring Cell Painting Features by @gwaygenomics in Inferring Cell Painting Features #42
• Add whitening by @gwaygenomics in Add whitening #43
• Refactor Before PooledCellPainting by @gwaygenomics in Refactor Before PooledCellPainting #44
• Adding PooledCellPainting by @gwaygenomics in Adding PooledCellPainting #45
• Add Init File in Pooled by @gwaygenomics in Add Init File in Pooled #46
• [Pooled] try to convert columns to numeric by @gwaygenomics in [Pooled] try to convert columns to numeric #47
• Adding MODZ Consensus Signature Operation by @gwaygenomics in Adding MODZ Consensus Signature Operation #53
• Fixing MODZ to behave properly when not all metadata columns are specified by @gwaygenomics in Fixing MODZ to behave properly when not all metadata columns are specified #55
• Add write_gct function by @gwaygenomics in Add write_gct function #56
• Upgrading Audit Functionality by @gwaygenomics in Upgrading Audit Functionality #60
• Functionality to Drop Outlier Features by @gwaygenomics in Functionality to Drop Outlier Features #62
• Fix aggregate dtype bug by @gwaygenomics in Fix aggregate dtype bug #65
• Remove kwargs everywhere by @gwaygenomics in Remove kwargs everywhere #66
• Allowing feature and metadata feature setting in write_gct by @gwaygenomics in Allowing feature and metadata feature setting in write_gct #67
• Add Feature Metadata to writing gct file by @gwaygenomics in Add Feature Metadata to writing gct file #68
• Adding Robust Normalization by MAD by @gwaygenomics in Adding Robust Normalization by MAD #72
• Fix mad_robustize policy on low variance columns by @gwaygenomics in Fix mad_robustize policy on low variance columns #74
• Enable cell counting with more than 2 defined strata by @gwaygenomics in Enable cell counting with more than 2 defined strata #76
• Add CMAP options to annotate by @gwaygenomics in Add CMAP options to annotate #73
• Abstract loading profiles and platemap by @gwaygenomics in Abstract loading profiles and platemap #84
• Adding CSV sniffing for delimiters by @gwaygenomics in Adding CSV sniffing for delimiters #85
• Fix missing value in variance threshold error by @gwaygenomics in Fix missing value in variance threshold error #86
• Fix write_gct too much strip by @gwaygenomics in Fix write_gct too much strip #87
• Switch to "samples='all'" as default and move operations to subfolder by @gwaygenomics in Switch to "samples='all'" as default and move operations to subfolder #88
• Updating whitening implementations by @gwaygenomics in Updating whitening implementations #91
• clean pycytominer folder base to include core functionality by @gwaygenomics in clean pycytominer folder base to include core functionality #92
• changed whiten_method default by @AdeboyeML in changed whiten_method default #97
• Fix gzip sniffer by @gwaygenomics in Fix gzip sniffer #98
• Refactor the consensus.py file to keep consistent API by @gwaygenomics in Refactor the consensus.py file to keep consistent API #101
• Change whiten nomenclature to spherize by @gwaygenomics in Change whiten nomenclature to spherize #102
• increase modularity of infer_cp_features by @hillsbury in increase modularity of infer_cp_features #103
• Setting up auto documentation with sphinx by @gwaygenomics in Setting up auto documentation with sphinx #104
• Updating theme and fixing RTD integration by @gwaygenomics in Updating theme and fixing RTD integration #105
• Adding pytest to requirements by @gwaygenomics in Adding pytest to requirements #106
• documentation edits by @bethac07 in documentation edits #108
• Adding single cell module by @gwaygenomics in Adding single cell module #111
• Updating consensus.py to also work with input files by @gwaygenomics in Updating consensus.py to also work with input files #115
• Output compression to ignore timestamps by @gwaygenomics in Output compression to ignore timestamps #119
• Subsampling at the point of single cell merging by @gwaygenomics in Subsampling at the point of single cell merging #121
• Refactoring annotate by @gwaygenomics in Refactoring annotate #118
• Fixing sphinx docs by @gwaygenomics in Fixing sphinx docs #124
• [hotfix] rename requirements doc by @gwaygenomics in [hotfix] rename requirements doc #125
• Adding epsilon parameter to spherize by @gwaygenomics in Adding epsilon parameter to spherize #132
• Fix aggregate dropping samples by @gwaygenomics in Fix aggregate dropping samples #134
• Modify aggregate by @niranjchandrasekaran in Modify aggregate #129
• Adding open source guideline documents by @gwaygenomics in Adding open source guideline documents #136
• Update README with Cell Painting paper URL by @shntnu in Update README with Cell Painting paper URL #139
• Set default object_feature to Metadata_ObjectNumber by @niranjchandrasekaran in Set default object_feature to Metadata_ObjectNumber #143
• Adding pipeline figure and boosting README by @gwaygenomics in Adding pipeline figure and boosting README #145
• Adding functionality to aggregate and annotate DeepProfiler output by @gwaygenomics in Adding functionality to aggregate and annotate DeepProfiler output #78
• Replace travis with github actions by @niranjchandrasekaran in Replace travis with github actions #151
• Replace aggregate_args by @niranjchandrasekaran in Replace aggregate_args #148
• Update DeepProfiler Processing by @michaelbornholdt in Update DeepProfiler Processing #149
• add citation note by @gwaygenomics in add citation note #157
• cells.aggregate_compartment() queries the database in chunks, reducing memory by @sjfleming in cells.aggregate_compartment() queries the database in chunks, reducing memory #156
• Add "noise removal" feature selection by @ruifanp in Add "noise removal" feature selection  #153
• fix issue when some samples have replicates and some don't by @bethac07 in fix issue when some samples have replicates and some don't #166
• Image features by @niranjchandrasekaran in Image features #168
• Add Metadata_ prefix to count features in the image table by @niranjchandrasekaran in Add Metadata_ prefix to count features in the image table #171
• update pipeline by @michaelbornholdt in update pipeline #163
• Remove step where image feature groups are capitalized by @niranjchandrasekaran in Remove step where image feature groups are capitalized #173
• Citation.cff by @gwaygenomics in Citation.cff #182
• Fix dataframe reference in SingleCells function by @gwaygenomics in Fix dataframe reference in SingleCells function #183
• Add explicit documentation for variance_threshold freq_cut and unique_cut by @gwaygenomics in Add explicit documentation for variance_threshold freq_cut and unique_cut #184
• Update doc style by @gwaygenomics in Update doc style #185
• Add github action to publish to pypi by @staylorx in Add github action to publish to pypi #188

New Contributors

• @gwaygenomics made their first contribution in Adding Initial Functions #1
• @AdeboyeML made their first contribution in changed whiten_method default #97
• @hillsbury made their first contribution in increase modularity of infer_cp_features #103
• @bethac07 made their first contribution in documentation edits #108
• @niranjchandrasekaran made their first contribution in Modify aggregate #129
• @shntnu made their first contribution in Update README with Cell Painting paper URL #139
• @michaelbornholdt made their first contribution in Update DeepProfiler Processing #149
• @sjfleming made their first contribution in cells.aggregate_compartment() queries the database in chunks, reducing memory #156
• @ruifanp made their first contribution in Add "noise removal" feature selection  #153
• @staylorx made their first contribution in Add github action to publish to pypi #188

Full Changelog: https://github.com/cytomining/pycytominer/commits/v0.1

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This discussion was created from the release Initial release of pycytominer.