Commit 114443b5 authored by Chris Evenhuis's avatar Chris Evenhuis
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# Yeast analysis script
### Clustering of cells
* RoI's for each cluster were hand drawn based on the phase image.
![](media/hand_roi.png)
* The clusters were segmented by seed based distance transformed watershed:
- Euclidean Distance Map was calculated for each RoI
- Seed points found as maxima on the distance distance map.
- Marker controlled watershed was performed using the seed points and the distance
![](media/cluster_seg.png)
This create a list of RoIs for each cell. This allowed each cell to assigned to a cluster and to measure the size and shape of each cell.
### Detecting of strings
To identify string structure in the GFP channel, for each cell RoI the following was performed:
- A White Top Hat transformation (MorhphoLibJ [1]) was performed on the GFP channel to enhance string-like features (disk of radius 5px).
- The 16-bit image was converted to 8-bit by setting maximum display range to 4 times the 97th percentile of the intensity distribution.
- Ridge Detect Plugin [2] was run to create RoIs for each filament
![](media/ridge_detection.png)
#### References
[1] Legland, D.; Arganda-Carreras, I. & Andrey, P. (2016), "MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ", Bioinformatics (Oxford Univ Press) 32(22): 3532-3534, PMID 27412086, doi:10.1093/bioinformatics/btw413
[2] Steger, C., 1998. An unbiased detector of curvilinear structures. IEEE Transactions on Pattern Analysis and Machine Intelligence, 20(2), pp.113–125.
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