OpenSource

This is for releasable software from Bioimage that has been published.

  • leverjs

    leverjs is the new new. it combines our previous LEVER and CloneView projects into a single set of software tools for working with live cell & tissue microscopy images.

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  • LEVER

    Open source lineage editing and validation tools for analysis of proliferating cells in phase-contrast microscopy.

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  • PixelRep

    source code for "Segmenting Touching Cells" manuscript is in review - code is NOT RELEASED FOR PUBLIC USE - this repository is only for use by selected reviewers code will be released free and open source when manuscript is accepted...

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  • lever-3d

    source code from E. Wait, et al., Visualization and Correction of Automated Segmentation, Tracking and Lineaging from 5-D Stem Cell Image Sequences. BMC Bioinformatics, 2014.

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  • rpe

    open source release for Joshi, et al., "Automated Measurement of Cobblestone Morphology for Characterizing Stem Cell-Derived Retinal Pigment Epithelial Cell Cultures", Journal of Occular Pharmacology and Therapeutics, In press, 2016.

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  • Organelle_Colocalization

    This is the source code for a manuscript currently under review. After the manuscript is accepted, the code will be available open-source (GPL v2). Until then, the code should only be viewed or downloaded by reviewers or editors for evaluation

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  • CloneView

    CloneView HTML5 viewer for LEVER - source from M. Winter, et al.,Computational Image Analysis Reveals Intrinsic Multigenerational Differences Between Anterior and Posterior Cerebral Cortex Neural Progenitor Cells, Stem Cell Reports (2015)

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  • bzlib2

    source code for static lib or dll bzip2 goes with the MultisetNCD, AITP and GapSpectral projects

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  • RAB-Tools

    source code from Clark, B., et al., Generation of Rab-based transgenic lines for in vivo studies of endosome biology in zebrafish. Developmental Dynamics, 2011. Blob tracker!

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  • MultisetNCD

    source code for A.R.Cohen and P.M.B. Vitanyi, Normalized Compression Distance of Multisets with Applications, IEEE Transactions on Pattern Analysis and Machine Intelligence. 2014.

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  • GapSpectral

    source code from A.R. Cohen, C. Bjornsson, S. Temple, G. Banker, and B. Roysam, "Automatic Summarization of Changes in Biological Image Sequences using Algorithmic Information Theory". IEEE TPAMI, 2009. 31(8)

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  • AxonTracker

    source code from "Axonal transport analysis using Multitemporal Association Tracking." Int J Comput Biol Drug Des. 2012;5(1):35-48.

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  • AITP

    source code for Algorithmic Information Theoretic Prediction and Discovery from Cohen et al., Computational prediction of neural progenitor cell fates, Nature Methods, 2010.

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