Links to open source tools for Analysis of Lightsheet data
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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/