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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.

Template to create new Icy plugin (POM file and base plugin class)

Toolbox to create and manipulate result tables with plug-ins and protocols, and export as text file or to your favorite spreadsheet software

description

The TensorFlow library manager plugin. This plugin allows users to choose the TF version to be used on runtime

Spot detector plugin for Icy

Active Contours plugin for Icy

HK-Means plugin for Icy

Track Manager plugin for Icy

MetroloSPIM plugin for Icy

Tools to measure tracking performance with the ISBI Challenge on Single-Particle Tracking metrics.

I adapted and copied code from by N. Chenouard, F. De Chaumon and S. Dallongeville so that it can run in batch and without Icy.

DeepLearning4J library for Icy. Website: https://deeplearning4j.konduit.ai/ Github: https://github.com/eclipse/deeplearning4j

Low-level functions for interactive communication between Icy and Matlab.

Export sequences from Icy to Matlab *.mat files

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.

Google FlatBuffers library for Icy https://github.com/google/flatbuffers