Schnitzcells

Schnitzcells is a MATLAB based software that allows for quantitative analysis of fluorescent time-lapse movies of living cells.  The software package is developed most specifically for bacteria and has been instrumental in analyzing  E.coli and B. subtilis movies (see publications).

The software contains functions that segment cells (based on either fluorescence or phase images), tracks cells in a frame-to-frame manner, and quantitatively extracts fluorescence.

The download page contains two links:  (1)  The current public version of Schnitzcells in a .zip archive and (2) A sample image set that we recommend using to test Schnitzcells.  The video tutorials page illustrate the analysis of this dataset and highlight the functionality and features of the software.

Please consider the following citation if Schnitzcells is used for publication:

Young,  J. W. , Locke,  J.C.W., Altinok, A., Rosenfeld, N., Bacarian, T., Swain, P.S., Mjolsness, E., Alon, U., Elowitz, M.B.  Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy. submitted to Nature Protocols.