Shantanu Singh

CellProfiler should support GCS URLs

8

Same as #3507. The issue came up with creating Terra workflows that run CellProfiler pipelines. The notes below are a slightly edited version of an [internal Slack conversation](https://broadinstitute.slack.com/archives/C033SCB245P/p1650903069288669) with @deflaux...

Upload Image Files to IDR

149

We will upload image files to the [Image Data Resource](https://idr.openmicroscopy.org/) and add URL and metadata information to the [Broad Bioimage Benchmark Collection](https://data.broadinstitute.org/bbbc/). We will use this issue to outline the...

Processing data using DeepProfiler

42

Juan asked this: I need to process the LINCS dataset to proceed with the plan we discussed for LUAD. I'm going to need access to the images, which is a...

Reprocess 10 plates because 36 features are missing

5

@EchteRobert reported this: Q about the LINCS dataset: I have run into plates which contain slightly fewer measured features than the bulk of the plates, i.e., 1745 instead of 1781....

Spherize is more intuitive and an accepted alternate term: https://en.wikipedia.org/wiki/Whitening_transformation

The vignette should be closer to this https://cytomining.github.io/profiling-handbook/create-profiles.html

Create a subpopulation report

1

The following RMD file contains the code to produce the PDFs containing the images of subpopulations which are enriched or de-enriched in a treatment. https://github.com/carpenterlab/2017_rohban_elife/blob/master/code/Cluster_Interpretation.Rmd Right now it is not...

Implement stepwise feature selection algorithm to remove linear dependencies

1

Similar to that described in Pg. 15 of http://bioconductor.org/packages/release/data/experiment/vignettes/DmelSGI/inst/doc/DmelSGI.pdf This will use output of #17 @shntnu needs to decide if this should be done on per-cell or per-well

Bug: explicit casting to DataFrame forces incorrect column names

1

### Example code with output In `normalize.normalize`, this chunk explicitly recreates a `pd.DataFrame` from `feature_df` ```py feature_df = pd.DataFrame( fitted_scaler.transform(feature_df), columns=feature_df.columns, index=feature_df.index, ) ``` This fails when the ` fitted_scaler.transform(feature_df).columns`...

Check if downloaded file is empty

1

# Description Thank you for your contribution to pycytominer! Please _succinctly_ summarize your proposed change. What motivated you to make this change? Please also link to any relevant issues that...