A tool to segment confocal microscope images

CellSeT is novel software that can be used to analyse confocal images of plant cells. Image analysis algorithms are used to extract the network structure of all cells. This information is then used to perform quantitative analysis on the cell structure, and additional analysis through the use of an extensible plug-in system. CellSeT is written in C# .NET, and as such runs only on Windows machines with an up-to-date version of the .NET framework installed. Plug-ins can be written in any .NET compatible language, such as C# or VB. For users who do not have access to a Windows machine, we have successfully used CellSeT in a virtual windows environment.

CellSeT has been published in a paper in The Plant Cell: CellSeT: Novel Software to Extract and Analyze Structured Networks of Plant Cells from Confocal Images. CellSeT is being released as open source. It can be downloaded from Sourceforge. We have produced documentation that outlines the use of CellSeT, and a detailed guide on writing customised plug-ins. These can be found below.

Quick Start Guide

The quick start guide contains an introductory document and associated images. It is aimed at new CellSeT users, and will familiarise you with the basic functionality of the software. Download Here.

User Documentation

More detailed information on the software can be found in the user guide. Those who wish to write their own plug-ins are strongly encouraged to read the specific plug-in documentation available here. User Documentation | Plug-in Documentation


For further information on the software, please contact Michael Pound.

Associated Publication

Biomodels Repository
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