Cell-ID is an open-source software designed for segmentation and quantification of microscopy images of yeast cells. The program uses brightfield images to identify cells, assigns a unique identifier number to each cell, scores interior and boundary pixels, tracks the cells through time-series of images and, in conjunction with fluorescence images, calculates various cellular measures.


   Download and Installation Guide

   Running Cell-ID

   Input Images

   Segmentation Algorithm and Quantification

   Cell-ID Segmentation Parameters

   Output Files

Related Papers

[1] Bush, A., A. Chernomoretz, R. Yu, A. Gordon, and A. Colman-Lerner. 2012. Using Cell-ID 1.4 with R for Microscope-Based Cytometry. Curr Protoc Mol Biol Chapter 14:Unit14 18.

[2] Gordon, A., A. Colman-Lerner, T. E. Chin, K. R. Benjamin, R. C. Yu, and R. Brent. 2007. Single-cell quantification of molecules and rates using open-source microscope-based cytometry. Nat Methods 4:175-181.

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