GitLab

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.

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.

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.

Playing around with building social-graphs on Reddit

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.

Cuda Kernels with Mex wrapper to process 3-D images

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)

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...

helper functions for image read/write and import.

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

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.

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.

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

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)

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

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!

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.