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Welcome to the source code repository for the bioimage analysis group (https://bioimage.coe.drexel.edu). See specific licenses, and contact andyrcohen 'at' outlook.com for questions.

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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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  • 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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  • bzlib2

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

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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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  • cohenTalk

    a selection of recent presentations

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  • direct-5D-viewer
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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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  • hydra-image-processor

    Cuda Kernels with Mex wrapper to process 3-D 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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  • 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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  • 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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  • leversc

    Project source and documentation for "LEVERSC: Cross-Platform Scriptable Multichannel 3-D Visualization for Fluorescence Microscopy Images"

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  • leverUtilities

    helper functions for image read/write and import.

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  • ljsctc
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  • llsm-calcium-vesicles-lever

    This project contains analysis source code for the publication: Winter et al., Dynamics and molecular control of calcium-vesicle motion during sea urchin skeletogenesis revealed by 4D lattice-light-sheet-microscopy, 2020.

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  • MAT
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  • MBL2016
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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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  • ncd

    repository for paper in review. code will be released free and open source (license tbd) when manuscript is accepted. contact andyrcohen@outlook.com for more info.

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  • NWD

    source code for 'Web Similarity', A. R. Cohen and P. M. B. Vitanyi. In review. Intended for review evaluation only. Not licensed for public use. Will be released free and open source on acceptance of manuscript.

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