CellProfiler workshop
The content of this workshop is primarily aimed to beginners, with the objective that at the end, the student understands basic concepts of high-content screening and analysis, and can produce basic pipelines in CellProfiler.
Below is the material that was provided to the students. It was made as a step-by-step protocol so that people unable to attend the workshop would have a chance to learn its content on their own. There is also a recording of a live session.
Archive containing the course material (presentations and input/output images)
The duration of the live workshop was approximately 3.5h with breaks and troubleshooting.
Before starting with the module, we suggest you to watch these good videos about digital images and image analysis:
Basics of digital images (e.g. concepts of bit-depth, color image, histogram), related to task 1:
https://www.ibiology.org/talks/digital-images/
Basics of image analysis (e.g. concepts of illumination correction, thresholding), related to tasks 2-4:
https://www.ibiology.org/talks/image-analysis/
The workshop contains several parts that should be read/completed in the following order:
NOTE: Using the preview mode for Powerpoint presentations alters the display. It is advised to download the presentation and open it using Powerpoint.
1- Introductory word document ():
- what is the goal of the workshop
- presentation of the content
- software packages needed
2- General presentation part 1 ( and course recording):
- Concept of high-content screening
- What is CellProfiler?
- Presentation of the fixed modules of CellProfiler
3- Task 1: GrayscaleToRGB ( and course recording):
- Task1 powerpoint presentation "GrayscaleToRGB"
- folders containing input and output images, the pipelines
- Recording of the workshop
4- General presentation part 2 ( and course recording):
- Concepts of image image segmentation, pre-processing, and illumination correction
- Presentation of the biological question addressed with the pipelines produced in the workshop
5- Task 2: Illumination correction ( and course recording):
- Task2 powerpoint presentation "Illumination correction"
- folders containing input and output images, the pipelines
- example pipeline with the illumination correction for 4 different channels
- Recording of the workshop
6- Task 3: Artificial image generation ( and course recording):
- Task3 powerpoint presentation "artificial image generation"
- folders containing input and output images, the pipeline
- Recording of the workshop
7- Task 4: Segmentation and feature extraction ( and course recording):
- Task4 powerpoint presentation "segmentation and feature extraction"
- The input images for task 4 are the input and output images from task 3
- folders containing output images, output spreadsheets, the pipeline
- An extra example pipeline used in a real experiment
- Recording of the workshop