This Indico installation shall not be used to organise MPI-CBG courses and events from beginning of 2024 on. Please use MPG Indico instead.

Cellprofiler Course

by Antje Janosch, Martin Stoter


CellProfiler Workshop:      

Mon, 28.11.2022 09:00 to 12:00; followed by a hands-on / bring your data session Wed, 30.11.2022 09:00 to 12:00

The Technology Development Studio (TDS) offers a hands on course on image analysis using CellProfiler.

CellProfiler is a free, open source software for quantitative analysis of biological images (
Advanced algorithms for image analysis, so called modules, are used to build an analytical pipeline in a GUI.
The pipeline can be used to identify objects and measure their features in thousands of images.
CellProfiler can be run on the HPC cluster for parallel processing of large image data sets.

Workshop content
-  Fundamental aspects of image analysis
-  Fundamental aspects of working with CellProfiler
-  Opening and importing images
-  Image manipulation (smoothing, enhancing features)
-  Segmentation and object detection (nuclei, cytoplasm, spots)
-  Relating and filtering objects
-  Measuring object features
-  Saving segmented images and result tables
-  Demo: CellProfiler on the HPC cluster

Participants should bring their own computers. No pre-knowledge or programming skills are needed. Software installation guides will be sent out later.

People with larger data sets a KNIME course could be of interest, as the output of CellProfiler can be easily analyzed with KNIME.
For people working in micro plate formats (96 well or 384 well) the KNIME Advanced/HCS Workshop would be useful as well.

Please registration here, for further information please contact the TDS (

For each Workshop we need to charge a fee of 150 € for internal registrants, and 250 € for external registrants.
Registration deadline is 4th of November. Places will be limited.
Until 10th of November, we will notify you if there is a place available for you in this round of workshops.

Organized by

TDS / Screening Faclility

Your browser is out of date!

Update your browser to view this website correctly. Update my browser now