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Icy is an open community platform for bioimage informatics

Bio-Formats library patched for Icy. The patch consist of replacing Apache Commons IO library by a newer version and also replacing org.json library with the custom version embedded into Micro-Manager to make it work properly.

Minimum Spanning Tree-based clustering

ROI blocks plugin for Icy. This plugin deliver a set of ROI tools to be used with Protocols (Graphical Programming).

Intensity projection plugin. It does intensity project along depth or time with multiple algorithms: mean, max, median, variance, standard deviation, saturated sum. Projection can also be restricted to ROI.

Image segmentation by representative colors selection. Two versions are available : – thresholding – positive and negative colors selection and SVM learning

My own toolbox used for all the plugins I developed.

A patched version of the Jama library. Internal structures accessors and package name added. The original version can be found here : http://math.nist.gov/javanumerics/jama/

Display the colormap over the image using an overlay.

Active Contours plugin for Icy