Decision Making in Living Cells
Ido’s talk at the Saturday Physics series
University of Illinois (October 2009).

Quantitative Adventures in Gene Regulation
Ido’s talk at the Workshop on Stochasticity in Biochemical Reaction Networks, Banff International Research Station (September 2013).

Skinner et al., Nat. Protoc. 2013


Spätzcells, also known as Spaetzcells, is a MATLAB program created to analyze fluorescence images obtained from single-molecule fluorescent in situ hybridization (smFISH) experiments in E. coli.

For citations and further information, please see Skinner et al., Nature Protocols 2013 (Paper webpage; PDF).


Spätzcells can be downloaded using this link (approx. 310 MB), which contains the following files:

  • Folder with Spätzcells code and analysis scripts.
  • Folder containing fluorescence images and segmentation masks to run the Spätzcells tutorial.
  • spatzcells_documentation.pdf: Instruction manual and tutorial.


MATLAB (The MathWorks), as well as the MATLAB Image Processing and Optimization toolboxes, are required to run this software. Spätzcells was developed using MATLAB versions 7.10 (R2010a) and 7.13 (2011b) (both 32 and 64 bits).


Watch how a figure in one of our publications (Sepúlveda et al., Science 2016, PDF) evolved over the course of 15 months. You may also download the PDF version of this process here.

See also: Tips for creating visually appealing graphics in MATLAB®, from the Golding Lab (PDF).