Cofilin rod formation (DRAFT)
Prerequisites
Before starting this lesson, you should be familiar with:
Learning Objectives
After completing this lesson, learners should be able to:
TODO
Motivation
TODO
Concept map
graph TD
ID("Image data") --> PP("Pre-processing")
PP --> IA("Image analysis")
IA --> SA("Statistical analysis")
Figure
Activities
Image analysis
Show activity for:
ImageJ Macro
Image analysis
The aim of this activity is to measure the formation of rod-like structures in the nuclei of cells in 3D.
This image analysis workflow consists of several steps, which may be adapted depending on the concrete implementation in a specific software package.
- Nuclei segmentation
- Thresholding of the 3D nuclei fluorescence image resulting in a binary mask
- Optionally running a fill holes algorithm on the binary mask
- Optionally separation of touching nuclei by a watershed
- Connected component labelling of the binary mask resulting in a label mask
- Rod segmentation
- Thresholding of the 3D rod fluorescence image resulting in a binary mask
- Connected component labelling of the binary mask resulting in a label mask
- Assignment of each rod to one nucleus
- Note that there are also rods outside nuclei should not be assigned to any nucleus
Show activity for:
CellProfiler
Image analysis
Show activity for:
R
Assessment
Fill in the blanks
- TODO ___ .
- TODO ___ .
Solution
- TODO
- TODO
Follow-up material
Recommended follow-up modules:
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