Essentials of Batch Image Analysis with CellProfiler

Christian Tischer   2020-06-25   Comments Off on Essentials of Batch Image Analysis with CellProfiler

Date(s) - 2020-06-25
09:30 CEST - 12:30 CEST

CellProfiler is a free and open-source software for batch image analysis. It requires no programming skills, yet has many powerful image modules that can be combined into a workflow.
For example, it has been used at EMBL’s ALMF for almost 10 years in more than 50 projects. It has been cited more then 6000 times and is thus one of the most popular image analysis software packages.

In this course you will learn the essentials of using CellProfiler for automated image analysis.


The course will be an online course; a corresponding zoom meeting link will be send to registered participants.


– CellProfiler user interface
– Image data import
– Object segmentation (e.g. detect nuclei in an image)
– Object feature measurements (e.g. measure size, shape and intensity of cells)
– Measurements export to a spreadsheet
– Creating and saving outline images
– Object relations (e.g. nuclei and cells and vesicles)

Participation requirements

– Basic understanding of microscopy, e.g. you regularly acquire image data on widefield or confocal fluorescence microscopes
– Basic understanding of scientific image data handling and inspection, e.g. you regularly inspect images using scientific software like ImageJ or python skimage
– No prior knowledge in image analysis is required


– Please install the latest version of CellProfiler on you computer:
– A link to download the course material will be send to registered participants shortly before the course starts.


Bookings are closed for this event.