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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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LSM Toolbox

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Shape Index Map

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TurboReg

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Linear Stack Alignment with SIFT

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Sigma Filter

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