plugin

ABSnake can segment complex structures in 2D images as well as 3D or temporal images. It uses a new active contour model based on a geometrical approach for correctly following invaginated structures.

MosaicIA is a tool to analyze the spatial distribution of objects in images. It estimates from an observed particle or object distribution what hypothetical interaction between the objects is most likely to have created this distribution.

ImageJ native "Skeletonize" implementation. - works only with 8-bit binary image. A faster implementation is available as a plugin Skeletonize3D written by Ignacio Arganda-Carreras. Pros of this plugin is summarized here.

Evaluates the orientation of fiber orientation pattern and plots the results in the image. It calculates gradient in x and y direction. - then calculates the eigenvector of nematic tensor, which is the orientation of the pattern.

## Short Summary Quote from the plugin page: >LineageTracker offers an ImageJ based framework which is easily extendible and has the capability to track cell lineages while being specifically designed to handle large cell displacements between frames. The methods are designed for fluorescent cells and have been used to analyse Schizosaccharomyces pombe, C2C12 mouse stem cells or migrating RPE cells. This tool also allows flexible cell segmentation and extendable in all aspects. The webpage is detailed with usage from ImageJ macro. Rather than being simply a component, the plugin is indeed a framework with set of components. ## Misc info A tip from the plugin author in ImageJ mailing list (08.Sep.2015): > We have an additional script to export only a selected range of frames. I can send you that if you think LineageTracker is something for you. To be on the safe side I would try it with an older version of ImageJ. We have experienced some problems, mostly related to Java. Java 8 seems to fix most of it. ## References 2630: Application example. 2631: Plugin Paper.

The GDSC Single Molecule Light Microscopy (SMLM) plugins is a package of tools for single molecule localisation analysis. - Fitting Plugins: get point cloud from super resolution image. - Results Plugins: organize results. - Analysis plugins - Model plugins

## Algorithm See .

A convenient tool for detecting lines! After the detection, detected lines are overlaid to the image. The plugin also stores these lines as ROIs, which could then easily be analyzed as vector information. Instead, the list of coordinates of all detected lines are placed in "contour" table. This could be used for redrawing or converting them as arrays. ## Algorithm See 2615.

A more modern approach for denoising / smoothening before segmentation, works like Gaussian blurring but preserves edges and boundaries. Listed in Fiji update sites. ## Algorithm Algorithm description is in [this page](http://www.ipol.im/pub/art/2011/bcm_nlm/) 2612. ## Example usage Localization of Membrane bound protein in Arabidopsis meristem was analyzed using the non-local-mean filter for refining its position 2613. ## impression It's effect is somewhere between Gaussian blurring and anistropic diffusion.

Adiposoft is an automated Open Source software for the analysis of adipose tissue cellularity in histological sections.

Example data can be found on the plugin description page in ImageJ wiki (download link). There is also a link to a MATLAB version of the workflow.