Running CellProfiler with OMERO.blitz

This document shows how to run  CellProfiler, an open source project to analyse and segment fluorescence microscopy images.

From the CellProfiler Website

CellProfiler cell image analysis software is designed for biologists without training in 
computer vision or programming to quantitatively measure phenotypes from thousands of 
images automatically. 

OMERO.cellprofiler supplies the OMEROJava connector and CellProfiler version 1.0 modules and subfunctions to download images from OMERO.blitz to CellProfiler and upload those images back to OMERO.blitz as a derived image of the original image.

WARNING

OMERO.cellprofiler is no longer tested (since the 4.2.x series), we will be soon working on a new version compatible with CellProfiler version 2.0

Installing the OMERO.cellprofiler

To install the modules required by CellProfiler, to work with OMERO.blitz you need to download

• download CellProfiler source from  CellProfiler.
• install wiki:OmeroMatlab
• copy the files from OMERO svn components/tools/cellprofiler
  • CPsubfunctions/CPOMEROimread.m
  • Modules/OMEROLoader.m
  • Modules/UploadImages.m
  • Modules/UploadMask.m
  • Modules/PlateLoader.m
  • Modules/LoadSingleImage.m
• include the files in components/tools/OmeroM to your matlab path

The OMEROLoader Module

The OMEROLoader module specifies where CellProfiler should retrieve images from.

PlateLoader Module

The PlateLoader Module downloads all images from a plate into CellProfiler.

SingleImageLoader Module

The SingleImageLoader Module downloads a single images with the specified id into CellProfiler.

OMERO Specific

The OMEROLoader, PlateLoader and SingleImageLoader requires you to specify the path to the ice.config file, the dataset id to retrieve images from and username and password.

Image Related

The image is specified by the mapping between the name of the channel and the channel index.

UploadMask Module

The UploadMask Module will upload the segmented images to OMERO as ROI on the original image.