Merge pull request #140 from fefossa/issues/138

Comments on Flags for # PLUGINS in config.py

Author: ErinWeisbart

config.py

@@ -41,8 +41,8 @@
 NECESSARY_STRING = ''        #Is there any string that should be in the file name to "count"?
 
 # PLUGINS
-USE_PLUGINS = 'False'
-UPDATE_PLUGINS = 'False'
-PLUGINS_COMMIT = '' # What commit or version tag do you want to check out?
-INSTALL_REQUIREMENTS = 'False'
-REQUIREMENTS_FILE = '' # Path within the plugins repo to a requirements file
+USE_PLUGINS = 'False'        # True to use any plugin from CellProfiler-plugins repo
+UPDATE_PLUGINS = 'False'     # True to download updates from CellProfiler-plugins repo
+PLUGINS_COMMIT = ''          # What commit or version tag do you want to check out?
+INSTALL_REQUIREMENTS = 'False' # True to install REQUIREMENTS_FILE defined below. Requirements should have all plugin dependencies.
+REQUIREMENTS_FILE = ''       # Path within the CellProfiler-plugins repo to a requirements file

documentation/DCP-documentation/advanced_configuration.md

@@ -23,3 +23,20 @@ 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 in config.py as `bethcimini/distributed-cellprofiler:2.1.0_4.2.4_plugins`.
+* **Custom model: If using a [custom User-trained model](https://cellpose.readthedocs.io/en/latest/models.html) generated using Cellpose, add the model file to S3.
+We use the following structure to organize our files on S3.
+```
+   └── <project_name>
+      └── workspace
+           └── model
+               └── custom_model_filename
+```
+* **RunCellpose module:** 
+    * Inside RunCellpose, select the "custom" Detection mode.
+    In "Location of the pre-trained model file", enter the mounted bucket path to your model. 
+    e.g. **/home/ubuntu/bucket/projects/<project_name>/workspace/model/**
+    * In "Pre-trained model file name", enter your custom_model_filename