cell tracking

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kota's picture

CellTrack

A standalone cell tracking software for single cell migration [1]. Tracking of cells in tissue was also done in Drosophila germband [2].

Download (or make in Linux)

See http://bio.cse.ohio-state.edu/CellTrack/

dscho's picture

Imaris

Imaris is a software for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy images. It performs interactive volume rendering that lets users freely navigate even very large datasets (hundreds of GB). It performs both manual and automated detection and tracking of biological “objects” such as cells, nuclei, vesicles, neurons, and many more. ImarisSpots for example is a tool to detect “spherical objects” and track them in time series. Besides the automated detection it gives the user the ability to manually delete and place new spots in 3D space.

dscho's picture

FARSIGHT

A General purpose image processing toolkit written in C++ based on ITK, VTK, Qt, and Boost. Main features: algorithms for cell segmentation, cell tracing, cell tracking, and vessel tracing. Registration and mosaicing algorithms for large scale datasets. Visualization tools actively linked to inspect and edit results.
Strengths:
- Open-source, free, multi platform, code is highly parallelized, uses git for version control
- Large scale processing, also efficient visualization of such datasets.
- Active learning module for classification

dscho's picture

CellProfiler

CellProfiler is designed to enable biologists without training in computer vision or programming to quantitatively measure cell or whole-organism phenotypes from thousands of images automatically. The researcher creates an analysis pipeline from modules that find cells and cell compartments, measure features of those cells to form a rich, quantitative dataset that characterizes the imaged site in all of its heterogeneity.

Anonymous's picture

ilastik - Manual Tracking

Anonymous's picture

ilastik - Automatic Tracking

sommerc's picture

CellCognition

Introduction

Pages

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