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u-segment is a Matlab software package to do 2D cell segmentation. This package provides a series of methods to create masks for the movie which separate objects (e.g. cells) from the background. Masks are binary images which contain 1 where there is an object of interest (cell), and 0 where there is background.

Granger-causal inference of the lamellipodial actin regulator hierarchy by live cell imaging without perturbation,Cell Systems, 2022, 13(6):471-487.e8, written by Jungsik Noh, Tadamoto Isogai, Joseph Chi, Kushal Bhatt,Gaudenz Danuser.

Functional Hierarchy of Redundant Actin Assembly Factors Revealed by Fine-Grained Registration of Intrinsic Image Fluctuations,Cell Systems, 2015, 1(1):37-50, written by Kwonmoo Lee, Hunter L. Elliott, Youbean Oak, Alex Groisman, Jessica D. Tytell,Gaudenz Danuser.

It consists of 4 steps, including optional steps, to create cell masks:

1. Generate Summation Channel.

2. Segmentation.

   Current available Segmentation methods:

   • Thresholding
   • MSA (Multi-Scale Automatic) Segmentation
   • External Segmentation

3. Trembling Correction.

4. Mask Refinement.

Danuser Lab Website

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