Summary and Schedule
Introduction
This workshop will teach you how to use CellProfiler for nuclei and cell segmentation, as well as feature extraction. It is organised by the Danish Bioimaging Infrastructure, which is a network that provides services for bioimage analysis, including teaching workshops, setting up workstations and providing 1-on-1 support. It includes the Image Analysis Core Facility, which provides further help, for example by completing entire analysis projects. For more information, click here to learn more about the things IACF can help you with.
Together, we will analyse a small image dataset on the impact of a chemical compound on cell morphology. We will use CellProfiler to detect cells and measure their morphology, before exporting our results. Time permitting, you can then see how to use these results in the bonus episode!
| Setup Instructions | Download files required for the lesson | |
| Duration: 00h 00m | 1. Introduction to the BBBC021 dataset | What is the BBBC021 dataset? |
| Duration: 00h 10m | 2. Reading images |
How do we get started in CellProfiler? How do we teach CellProfiler the structure of our images? |
| Duration: 00h 27m | 3. Identifying primary objects |
How does CellProfiler identify objects in an image? Why do we usually start segmentation with nuclei? Which parameters matter most for good nucleus segmentation? |
| Duration: 01h 12m | 4. Identifying secondary & tertiary objects |
How can we detect whole cells once we have identified nuclei? What is the differences between detecting primary, secondary, and tertiary objects? |
| Duration: 01h 37m | 5. Measuring object intensity and shape |
Once we have segmentation masks, what can CellProfiler measure from
them? What is the difference between intensity measurements and shape measurements? |
| Duration: 02h 07m | 6. Reproducibility in CellProfiler |
What is the difference between saving a CellProfiler project and
exporting a pipeline? Which approach is more portable across computers and collaborators? |
| Duration: 02h 27m | 7. Bonus: visualising features |
How do you read CellProfiler’s exports? What information can be gleamed from them? |
| Duration: 02h 39m | 8. Advanced: classifying cells in CellProfiler Analyst |
How do you classify cells with CellProfiler Analyst? What files do you need to move from CellProfiler to CellProfiler Analyst? How can you tell whether your classifier is performing well? |
| Duration: 03h 19m | Finish |
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.
Setup
For this workshop, you will need to:
If you have any trouble with these steps, please let one of the teachers know so they can help you set this up before proceeding. Once you are ready, navigate to the exercise using the arrow buttons below.
If you already have CellProfiler installed, please check whether it
is the latest version. You can do so in CellProfiler by clicking
Help > About CellProfiler. The latest version as of
February 2026 is 4.2.8. If you have version 4.2.0 or newer this workshop
should work for you, though you may see a warning during the
reproducibility episode, which can be ignored. If you have an older
version, please install the latest version of CellProfiler before
starting this workshop.
Help
If you get stuck at any step, first try to solve the issue yourself or with the help of an instructor. If needed, you can also download a working version of the pipeline here:
You may have to right click the button and select “Save Link As…”.
After downloading the pipeline, you can compare it to yours for
troubleshooting. To do so, first open a new CellProfiler window. Then,
import this pipeline in CellProfiler by clicking on File
> Import > Pipeline from File.
Further information
A lot of the information covered in this workshop are also covered in the Ask Erin Dear Beth podcast series, a fantastic resource by Erin Weisbart and Beth Cimini.
CellProfiler also has a number of tutorials, like this one on segmentation. And it also comes with extensive documentation, found here.