Add cellpose explanation to documentation

Author: fefossa

documentation/DCP-documentation/advanced_configuration.md

@@ -23,3 +23,18 @@ These values can be modified in run.py .
 * **Frequency or types of information included in the per-instance logs:** These can be adjusted in the instance-monitor script.
 * **[CellProfiler command line flags](https://github.com/CellProfiler/CellProfiler/wiki/Adapting-CellProfiler-to-a-LIMS-environment#cmd):** These can be modified in the cp-worker script.
 * **Log stream names or logging level:** These can be modified in the cp-worker script.
+
+## Changes to CellProfiler pipeline to use Distributed-CellProfiler with Runcellpose plugin
+
+* **Distributed-CellProfiler version:** At least CellProfiler version 4.2.4, and use the DOCKERHUB_TAG on config.py as `bethcimini/distributed-cellprofiler:2.1.0_4.2.4_plugins`.
+* **Custom model:** the user could be interested in using a [User-trained model](https://cellpose.readthedocs.io/en/latest/models.html).  
+    * **AWS:** If using custom model generated using cellpose, add the model file to the folder in the following structure:
+```
+   ├── <project_name>
+   ├── workspace
+   │   ├── model
+   │   │   ├── custom_model_filename
+```
+* **RunCellpose module:** 
+    * Inside RunCellpose you should select the Detection mode to "custom". Then, it will ask you for "Location of the pre-trained model file". There paste the path (adapted to your project): **/home/ubuntu/bucket/projects/<project_name>/workspace/model/**
+    * Paste the custom_model_filename to "Pre-trained model file name" field.