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Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh

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Workflow URL: 
Workflow Author: 

Rizk A, Paul G, Incardona P, Bugarski M, Mansouri M, Niemann A, Ziegler U, Berger P, Sbalzarini IF

Dependencies: 
Workflow Language: 
Dimension: 
3D
Input data type: 
single image (for segmentation), two channel image (for colocalization)
Output data type: 
segmentation image, colocalization summary (csv file)
Example Image URL: 
Comment / Instructions: 

This Fiji plugin, Squassh, its workflow and protocol is described in [1]. It enables detecting, segmenting, and quantifying subcellular structures in fluorescence 2D/3D microscopy images. For segmentation, it accounts for the microscope optics and for uneven image background. Further analyses include both colocalization and shape analyses. However, it does not work directly for time lapse data. A brief summary note can be found here.

References

  1. [2506] Rizk A, Paul G, Incardona P, Bugarski M, Mansouri M, Niemann A, Ziegler U, Berger P, Sbalzarini IF
    2014.  Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh.. Nat Protoc. 9(3):586-96.
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