Featurization of new segmentation makss (#107)

* ready for HPC

* runnnig features:

* run on HPC

* loadfile upload

* rtd

* rtd remove for another feature branch

* new rerun file:

* waiting on run

* run on HPC

* rerun on HPC

* complete runs on HPC

* run on HPC

* run the combinations

* all features are run

* rerun organoids on HPC

* fix resources calls for HPC

* Update 3.cellprofiling/local_run_GPU_DL_features.sh

Co-authored-by: Jenna Tomkinson <[email protected]>

* Update 3.cellprofiling/local_run_GPU_DL_features.sh

Co-authored-by: Jenna Tomkinson <[email protected]>

* Update 3.cellprofiling/scripts/get_run_combinations_convolved_data.py

Co-authored-by: Jenna Tomkinson <[email protected]>

* addressing comments

* addressing comments

---------

Co-authored-by: Jenna Tomkinson <[email protected]>

Author: MikeLippincott

.pre-commit-config.yaml

@@ -16,7 +16,7 @@ repos:
     #Code formatter for both python files and jupyter notebooks
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.14.13
+    rev: v0.14.14
 
     hooks:
       # Run the formatter.

0.preprocessing_data/README.md

@@ -89,6 +89,7 @@ Please see the `nyquist_sampling_calculations.ipynb` notebook for the calculatio
 | NF0030_T1 | C6-4 | removed | Unnest failure |
 | NF0030_T1 | D4-7 | removed | Unnest failure |
 | NF0035_T1 | E9-3 | removed | Unnest failure |
+| SARCO361_T1 | D2-3 | removed | Unnest failure |
 
 
 ## Yokogawa CQ1 vs Echo analysis and key differences