Contents

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.

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.

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.

Estimate the frequency of hepatitis C virus infected cells based on the intensity of viral antigen associated immunofluorescence. 

The core is an ImageJ Macro, so it's easy to modify for one's own needs (Link to the code). 

ImageJ macro for the morphometry of neurites. > NeurphologyJ; it is capable of automatically quantifying neuronal morphology such as soma number and size, neurite length, neurite ending points and attachment points. NeurphologyJ is implemented as a plugin to ImageJ, an open-source Java-based image-processing and analysis platform.

An object detection function in ImageJ. [Analyze > Analyze Particles...]. It could simply be used for counting number of cells, but could also do more complex stuffs. ## Jython Snippet Here is a snippet of how to use Particle Analysis in Jython script.

A resident function in ImageJ, located in the menu as [Process > Binary > Voronoi].

Quote from the ImageJ reference page:

The Virtual Brain Explorer (ViBE-Z) is a software that automatically maps gene expression data with cellular resolution to a 3D standard larval zebrafish (Danio rerio) brain. It automatically detects 14 predefined anatomical landmarks for aligning data. It also offers a database and atlas. The ViBE-Z database, atlas and software are provided via a web interface. A data preparation step is needed in order to provide the right input data and format.

Auto-Bayes is a software package based on Bayesian statistics and requires no user dependent parameters for molecule detection and image reconstruction for Single-Molecule Localization Microscopy (SMLM), including photoactivated localization microscope (PALM), stochastic optical reconstruction microscope (STORM), and direct stochastic optical reconstruction microscopy (dSTORM), etc.

This software is designed for the rapid semi-automatic detection and quantification of synaptic protein puncta from 2D immunofluorescence images generated by confocal laser scanning microscopy.

- 2D Stabilization in each slice of the stacks in time. - 3D Stabilization intravital imaging of all the stacks (including the dimension Z) - create the videos and the stabilized images in a new folder 2701

PSF Lab is a software program that calculates the illumination point spread function of a confocal microscope under various imaging conditions. It is available in 32-bit and 64-bit for Windows and in 64-bit for Mac.

FOCAL (Fast Optimized Cluster Algorithm for Localizations) is a rapid density based algorithm for detecting clusters in localization microscopy datasets.

WaveTracer is a plugin for Metamorph. It represents a functional method for real-time reconstruction with automatic feedback control, without compromising the localization accuracy. It relies on a wavelet segmentation algorithm, together with a mix of CPU/GPU implementation.

Clus-Doc is a software that quantifies both the spatial distribution of a protein as well as its colocalization status. It may be used to quantify signaling activity and protein colocalization at the level of individual proteins.

This plugin allows : Calculating co-localization between objects in 3D Measuring 3D distances between nearest object, co-localized or not Getting some 3D measurements about each objects The plugin can be used with labelled images, but it also integrates tools for the segmentation of the objects. Programming language: JAVA Processes: Denoise filter Segmentation of the objects Object based co-localization and distance analysis Counting and measurements on objects

This is the source code and data page of a distributed parallel algorithm 2683 for segmentation of large fluorescence microscopy images.

Image-processing algorithms developed at the MOSAIC Group for fluorescence microscopy. Tools included: