Links to open source tools for Analysis of Lightsheet data

Owned by Ofra Golani
Last updated: Apr 24, 2017
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OpenSegSPIM:

Open access and user friendly 3-D automatic quantitative analysis tool for nuclei and cell membranes.

Publication: http://bioinformatics.oxfordjournals.org/content/32/13/2075.short

URL: http://opensegspim.weebly.com/


RACE:

Real-time Accurate Cell-shape Extractor (RACE), a high-throughput image analysis framework for automated three-dimensional cell segmentation in large-scale images. 

From Keller's lab 

Publication: http://www.cell.com/developmental-cell/pdf/S1534-5807(15)00837-0.pdf

URL: https://bitbucket.org/jstegmaier/race/overview


Cell lineages from large-scale fluorescence microscopy data

Automated modules of the cell lineaging framework, Modified CATMAID module for visualizing image and cell lineage data, manually curating cell lineage data and annotating cell lineage reconstructions

Publication: http://www.nature.com/nmeth/journal/v11/n9/full/nmeth.3036.html


ImSAnE (Image Surface Analysis Environment)

Tissue cartography, and the open-source MATLAB toolbox ImSAnE (Image Surface Analysis Environment) implementing it as a a practical tool for compression and analysis of arbitrarily shaped Surfaces Of Interest in layered bio-image data

Publication: http://www.nature.com/nmeth/journal/v12/n12/full/nmeth.3648.html

URL: http://www.tissuecartography.org/