Contents

The purpose of the workflow is ....

First you need

Drishti (from Sanskrit  word for "vision" or "insight") is a multi-platform, open-source volume-exploration and presentation tool. Written for visualizing tomography data, electron-microscopy data and the like.

  FlyLimbTracker is  a method that uses active contours to semi-automatically track body and leg segments from video image sequences of unmarked, freely behaving Drosophila flies. This approach can be used to measure leg segment motions during a variety of locomotor and grooming behaviors.

For now the plugin have to be downlaoded directly from the EPFL website (see link), not from the search bar as usual in ICY.

Several algorithm for cell tracking were described and benchmarked for different data sets types. Please do through them and check if any tools is not tagged yet and add them, if already here, put the comparison paper

please ? www.celltrackingchallenge.net/ 

https://www.nature.com/articles/nmeth.4473?WT.feed_name=subjects_image-… 

Classification of trajectoire: need tracking results as input and will then classify the trajectories as  brownian motion, confined brownian or directed.

Reconstruct big images from overlapping tiled images on a Spark cluster.

The code is based on the Stitching plugin for Fiji https://github.com/fiji/Stitching

Working version of a simple GUI frontend for CMTK image registration tools in Fiji

Estimate the positions and spacing between sections (or at local points) of three dimensional image data. This method may be applied to any imaging modality that acquires 3-dimensional data as a stack of 2-dimensional sections. We provide plugins for both Fiji and TrakEM2.

"An open source machine learning framework for everyone "

Super-resolve anisotropic EM data along low-res axis with deep learning.

The MIPAV (Medical Image Processing, Analysis, and Visualization) application enables quantitative analysis and visualization of medical images of numerous modalities such as PET, MRI, CT, or microscopy. Using MIPAV's standard user-interface and analysis tools, researchers at remote sites (via the internet) can easily share research data and analyses, thereby enhancing their ability to research, diagnose, monitor, and treat medical disorders.

Multicut workflow for large connectomics data. Using luigi for pipelining and caching processing steps. Most of the computations are done out-of-core using hdf5 as backend and implementations from nifty

Luigi is a Python module that helps you build complex pipelines of batch jobs. It handles dependency resolution, workflow management, visualization etc. It also comes with Hadoop support built in.

ANTs computes high-dimensional mappings to capture the statistics of brain structure and function.

A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O.