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!



Anonymous's picture

OrientationJ

volker's picture

FISH-quant

Workflow Language: 
MATLAB
volker's picture

jicbioimage

The jicbioimage [1] Python package makes it easy to explore microscopy data in a programmatic fashion. Exploring images via coding means that the exploratory work becomes recorded and reproducible. Furthermore, it makes it easier to convert the exploratory work into (semi) automated analysis work flows.

Features Built in functionality for working with microscopy data Automatic generation of audit trails IPython integration Cross-platform: Linux, Mac and Windows are all supported Works with Python 2.7, 3.3 and 3.4

Anonymous's picture

Squassh

kota's picture

InfectionCounter

Workflow Language: 
ImageJ Macro Language
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Voronoi ImageJ

Package/Library: 
ImageJ
czhang's picture

TurtleSeg: 3D Image Segmentation Software

TurtleSeg is an interactive 3D image segmentation tool. TurtleSeg has an automated system, Spotlight, for automatically directing the user towards the next steps. Typically, a user loads a 3D image and then manually contour a sparse number of slices, the full 3D segmentation can then be built automatically.

aaron's picture

IceImarisConnector

IceImarisConnector is a simple commodity class that eases communication between Bitplane Imaris and MATLAB or python using the Imaris XT interface.

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