Skip to content

Commit

Permalink
Browse files Browse the repository at this point in the history
  • Loading branch information
gwaybio committed Jun 23, 2023
1 parent a5dc867 commit 9ac7c78
Showing 1 changed file with 3 additions and 0 deletions.
3 changes: 3 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -114,6 +114,9 @@ Therefore, we have included some custom tools in `pycytominer/cyto_utils` that p
- [Cell locations lookup table generation](#Creating-a-cell-locations-lookup-table)
- [Generating gct files for Morpheus visualization](#Generating-a-GCT-file-for-morpheus)

Note, [`pycytominer.cyto_utils.cells.SingleCells()`](pycytominer/cyto_utils/cells.py) contains code to interact with single cell SQLite files, which are output from CellProfiler.
The single-cell processing speed of SQLite files depends on SQLite file size and amount of memory (RAM) available the computational environment machine.

### CellProfiler CSV collation

If running your images on a cluster, unless you have a MySQL or similar large database set up then you will likely end up with lots of different folders from the different cluster runs (often one per well or one per site), each one containing an `Image.csv`, `Nuclei.csv`, etc.
Expand Down

0 comments on commit 9ac7c78

Please sign in to comment.