CellECT is a tool for cell analysis in 3-D confocal microscopy membrane volumes. CellECT provides a segmentation tool, which runs seeded watershed on the volume, predicts uncertain areas and allows the user to interact with the segmentation in order to correct it. CellECT also provides a tracking tool for discovering cell lineage across multiple 3-D volumes.

Skip to CellECT Segmentation Tool

Skip to CellECT Tracking Tool

CellECT is supported for Linux and MacOS, and was tested on Ubuntu 11.10, Ubuntu 12.04 and Fedora 18.

Prerequisites:

• python 2.7
• numpy 1.6.1
• scipy 0.10.0
• python-image
• matplotlib 1.1.1 or above
• pyml 0.7.10 (and libsvm)
• termcolor
• pylibtiff (and libtiff)
• pyside wrapper for Qt
• opencv python wrappers
• matlab (needed for imimposemin, watershed)

An install script tested on Fedora 18 is provided here

After the prerequisites, CellECT can be installed as follows:

python setup.py build
python setup.py install

CellECT can be run from command line:

CellECT

CellECT can work with TIFF stacks which contain membrane channel (and optionally nuclei channel), at one or multiple time points. You can create a workspace from a new TIFF dataset, or you can open an existing workspace and continue working with it. A new workspace will optionally take as input the output of a nuclear detector as a .csv file. If no such file is provided, the user can manually add points later, or or opt for randomized input points.

Author:

Diana Delibaltov, Ph.D. student at the Vision Research Lab at University of California, Santa Barbara.

License:

Disclaimer:

I assume no responsibility for any effect this software may have on you, your family, pet, computer, or anything else related to you or your existance. No warranty provided nor implied.