View on GitHub

Image Analysis Group

We are the Image Analysis Group at the Francis Crick Institute. Images are essentially grids of numbers and image analysis allows for the translation of these numbers into insights. Talk to us about analysis prior to acquiring any image data - we're happy to provide all the training you need.

CellProfiler

CellProfiler is widely used here at the Crick to do segementation and quantification of images, without a lot of image analysis background. The documentation for CellProfiler can be found at the CellProfiler Wiki.

CellProfiler on HPC OnDemand

We’re beginning to experiementally support a GUI version of Cellprofiler on HPC OnDemand. This is very much a work in progress, but please feel free to beta test and tell us how it is working.

Requirements:

HPC OnDemand account (Contact HPC on the #HPC Slack Channel) to get your account set up.

You may find it useful to have your .conda and .cache home directories soft-linked to your working directory.

A bit of linux/command line experience would help for now. We’re hoping to make it easier

Files:

There are three files that are used for installation and running. You can download them from The CALM Github Page for CellProfiler.

install_cellprofiler.sh

run_cellprofiler.sh

Download_CellProfiler_Plugins.sh

To install :

ALL OF THIS NEEDS TO BE DONE IN ONDEMAND

Navigate to the folder where you downloaded the files.

Run the command “./install_cellprofiler.sh”

This will take between 5-10 minutes, depending on how many resources you asked for.

If all goes well, CellProfiler will download and be installed in a new mamba/conda environment. This should be reported by the install file at the end of the process

To Run:

In the directory in which you downloaded the run_cellprofiler.sh file, run the command

”./run_cellprofiler.sh” without the quotes

To Download and use plugins:

Make a directory to store the plugins in your working directory. The plugins are small python scripts, you do not need a lot of room.

In the directory where you downloaded the Download_CellProfiler_Plugins.sh run the command

”./Download_CellProfiler_Plugins.sh /path/to/your/folder” without the quotes, Where /path/to/your/folder is replaced by the path to the folder you made for the plugins

Open CellProfiler again using “./run_cellprofiler.sh”

Under “File” –> “Preferences” –> set the “CellProfiler plugins directory” to your plugins directory.