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Fiji

Fiji is just ImageJ: a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. The main focus of Fiji is to assist research in life sciences. It is a free, open-source, community-driven project.

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ImarisXT

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3D Area

Package/Library: 
Icy
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Maximum Entropy Threshold

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Grid

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Segmentation Editor

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Watershed

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Iterative Deconvolve 3D

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Series Labeler

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TurboReg

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