Add collate.py

README.md

@@ -45,8 +45,11 @@ Since the project is actively being developed, with new features added regularly
 # Example:
 pip install git+git://github.com/cytomining/pycytominer@2aa8638d7e505ab510f1d5282098dd59bb2cb470
 ```
+### CSV collation
 
-If you want to perform data collation inside pycytominer, you will need an extra package; this will change your installation commands slightly
+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. In order to look at full plates, therefore, we first need to collate all of these CSVs into a single file (currently SQLite) per plate. We currently do this with a library called [cytominer-database](https://github.com/cytomining/cytominer-database). 
+
+If you want to perform this data collation inside pycytominer using the `cyto_utils` function `collate` (and/or you want to be able to run the tests and have them all pass!), you will need `cytominer-database==0.3.4`; this will change your installation commands slightly
 
 ```bash
 # Example for general case commit:
@@ -55,6 +58,8 @@ pip install "pycytominer[collate] @ git+git://github.com/cytomining/pycytominer"
 pip install "pycytominer[collate] @ git+git://github.com/cytomining/pycytominer@2aa8638d7e505ab510f1d5282098dd59bb2cb470"
 ```
 
+If using `pycytominer` in a conda environment, you will also want to make sure to add `cytominer-database=0.3.4`to your list of `dependencies`.
+
 ## Usage
 
 Using pycytominer is simple and fun.