[Hot Fix] README figure wonk (#295)

* close #294 * close #198 * Update README.md Co-authored-by: Dave Bunten <[email protected]> * Update README.md Co-authored-by: Dave Bunten <[email protected]> * add alt description * remove comma --------- Co-authored-by: Dave Bunten <[email protected]>
cytomining · Jun 23, 2023 · 7320516 · 7320516
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Showing 1 changed file with 6 additions and 2 deletions.
diff --git a/README.md b/README.md
@@ -10,8 +10,9 @@
 Pycytominer is a suite of common functions used to process high dimensional readouts from high-throughput cell experiments.
 The tool is most often used for processing data through the following pipeline:
 
-<img height="500" src="https://github.com/cytomining/pycytominer/blob/master/media/pipeline.png?raw=true">
-[Click here for high resolution image](https://github.com/cytomining/pycytominer/blob/master/media/pipeline.png)
+<img height="325" alt="Description of the pycytominer pipeline. Images flow from feature extraction and are processed with a series of steps" src="https://github.com/cytomining/pycytominer/blob/master/media/pipeline.png?raw=true">
+
+[Click here for high resolution pipeline image](https://github.com/cytomining/pycytominer/blob/master/media/pipeline.png)
 
 Image data flow from a microscope to cell segmentation and feature extraction tools (e.g. CellProfiler or DeepProfiler).
 From here, additional single cell processing tools curate the single cell readouts into a form manageable for pycytominer input.
@@ -113,6 +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.
+Processing capabilities for SQLite files depends on SQLite file size and your available computational resources (for ex. memory and cores).
+
 ### 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.