BioImage Information Index

Biii is a website for organizing bioimage analysis resources. We manually edit following pages, for you to search tools, workflows and functions for bioimage analysis:

Please enjoy!



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Huygens Remote Manager

The Huygens Remote Manager is an open-source, efficient, multi-user web-based interface to the Huygens software by Scientific Volume Imaging for parallel batch deconvolutions.

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XuvTools

XuvTools (pronounced “ex-you-vee-tools”) is a fully automated 3D stitching software for biomedical image data, typically confocal microscopy images. XuvTools runs on Microsoft Windows XP and Vista, Linux and Apple Mac computers. It supports 32 and 64bit operating systems (with 64bit highly preferred). XuvTools is free and open source software (see Licensing), so you can start using it immediately. Go to Downloads and give it a try.

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Analyze Particles

Package/Library: 
Fiji
ImageJ
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Balanced SOFI

Super-resolution optical fluctuation imaging (SOFI) achieves 3D super-resolution by computing temporal cumulants or spatio-temporal cross-cumulants of stochastically blinking fluorophores [1,2]. In contrast to localization microscopy, SOFI is compatible with weakly emitting fluorophores and a wider range of blinking conditions [3]. Balanced SOFI analyses several cumulant orders for extracting molecular parameter maps, such as the bright and dark state lifetimes, the concentration and the brightness distributions of fluorophores within biological samples [a].

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FreeD

Free-D is a three-dimensional (3D) reconstruction and modeling software. It allows to generate, process and analyze 3D point and surface models from stacks of 2D images.

Free-D is an integrated software, offering in a single graphical user interface all the functionalities required for 3D modeling. It runs on Linux, Windows, and MacOS.

Free-D is developed by the Modeling and Digital Imaging team of the Institut Jean-Pierre Bourgin, INRA Versailles, France.

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PSF Lab

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ec-CLEM

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Morpholeaf

Package/Library: 
FreeD

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