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Elastix is a toolbox for rigid and nonrigid registration of (medical) images.

Elastix is based on the ITK library, and provides additional algorithms for image registration. 

The software can be run as a single-line command, making it easy to include in larger scripts or workflows. The user needs to edit a configuration file that contains all relevant parameters for registration: transformation model, metric used to comapre images, optimization algorithm, mutliscale pyramidal representation of images...

CaPTk is a software platform for analysis of radiographic cancer images, currently focusing on brain, breast, and lung cancer. CaPTk integrates advanced, validated tools performing various aspects of medical image analysis, that have been developed in the context of active clinical research studies and collaborations toward addressing real clinical needs.

NiftyNet is a TensorFlow-based open-source convolutional neural networks (CNNs) platform for research in medical image analysis and image-guided therapy. NiftyNet’s modular structure is designed for sharing networks and pre-trained models. Using this modular structure you can:

• Get started with established pre-trained networks using built-in tools;
• Adapt existing networks to your imaging data;
• Quickly build new solutions to your own image analysis problems.

This ParaViewWeb Docker container is used by the Galaxy Project.  Paraview is an VTK based visualization server, for 3D.

Image analysis tools to be used within Galaxy

Galaxy instance with tools for Image analyses shipped in a Docker container.

Orbit Image Analysis is a free open source software with the focus to quantify big images like whole slide scans.

It can connect to image servers, e.g. Omero.
Analysis can be done on your local computer or via scaleout functionality in a distrubuted computing environment like a Spark cluster.

Sophisticated image analysis algorithms incl. tissue quantification using machine learning, object segmentation and classification are build in. In addition a versatile API allows you to enhance Orbit and to run your own scripts.

HyphaTracker propose a workflow for time-resolved analysis of conidia germination. Each part of this workflow can also be used independnatly , as a toolbox. It has been tested on bright-field microscopic images of conidial germination.

LimeSeg: A coarsed-grained lipid membrane simulation for 3D image segmentation **Download instruction:** There is no download but you can easily install this plugin via ImageJ update site. If you really need to download the jar file, access the file in the update site repository ([Link]())

automated open-source image acquisition and on-the-fly analysis pipeline (initially developped for analysis of mitotic defects in fission yeast)

Computer-assisted Evaluation of Myelin formation (CEM) is a collection designed to automate myelin quantification. It requires use input to choose the best threshold values. The myelin is calculated as an overlap between neuronal signal and oligodendrocyte signal. Results are given as pixel counts and percents.

MaMuT is an end user plugin that combines the BigDataViewer and TrackMate to provide an application that allow browsing, annotating and curating annotations for large image data.

This filter uses convolution with a Gaussian function for smoothing. Sigma is the radius of decay to exp(-0.5) ~ 61%, i.e. the standard deviation sigma of the Gaussian (this is the same as in Photoshop, but different from earlier versions of ImageJ, where a value 2.5 times as much had to be entered.

Kymograph generation under ImageJ:

one simple solution, plot a line (ROI line) on the first frame, where you want to generate the kymograph.

Use

Image  / Stacks  / Reslice

It will generate a new image were Y dimension is the time, and X the position on the line you have drawn.

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.