Project Description


CellShape is a pixel-based image analysis tool that allows obtaining statistical information from cell microscopy images. It is used to quantify different events, which in the current version (v0.8) are:

– Identification of nucleoid regions and mRNA spots.
– Fluorescent inensity distribution (flow cytometry emulation).
– Outline segmentation.
– Correlation of regions in cells.
– Pixel itensity record.

Unlike other similar packages, CellShape is entirely Python-powered and independent from any third-party programmes. The main analytic routines make use of Python modules, maximizing the modularity of the code (ideal for developers willing to modify CellShape). Standalone executables are provided, which makes CellShape easy to use without installation.

Download the source from the following link:


Download the MacOSX version (tested from Lion to El Capitan) from the following link:


Download the Windows version (tested in Windows 7 and 8) from the following link:


A manual on how to use CellShape and a README file are included in all downloads.