Automated

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.

Quote:

The "Angiogenesis Analyzer" allows analysis of cellular networks. Typically, it can detect and analyze the pseudo vascular organization of endothelial cells cultured in gel medium

...a simple tool to quantify the ETFA (Endothelial Tube Formation Assay) experiment images by extracting characteristic information of the network.

The outputs are network feature parameters.

Sample images

http://image.bio.methods.free.fr/ij/ijmacro/Angiogenesis/HUVEC-Pseudo-Phase-Contrast.tif.zip

http://image.bio.methods.free.fr/ij/ijmacro/Angiogenesis/HUVEC-Fluo.tif.zip

Source code

https://imagej.nih.gov/ij/macros/toolsets/Angiogenesis%20Analyzer.txt

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

This workflow will batch process a directory of images: - comets should be horizontally oriented, tails to the right. Additional preprocessing is required if the gel does not match with this orientation (Rotate images, Using ImageJ/Transform Image or TransformJ plugin for example). Then using the plugin:

1. Uneven background correction
2. Automatic detection of comet shapes with outliers detection
3. Automatic detection of the heads of comets (brightest region or profile analysis)
4. Statistical values of tails, heads and Olive moments.

• Manual correction is available.
• Does live analysis with Micro-Manager

## Algorithm See .

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.

## About TANGO software is an open-source software for Analysis of Nuclear Genome Organization. It is composed of an ImageJ plugin for batch processing and analysis, and a R package for statistical analysis. Reference: 2528 ## Some key features - Image import uses bioimage formats. - Construction of workflow in GUI by choosing filters / segmentation strategy for - Prefiltering - Segmentation - Postfiltering - Isolated nuclei could individually be inspected, deleted from list and subjected for detailed analysis. - Uses MCIB3D library as backend. - Basic usage is to segment nucleus, crop them to single nucleus objects, segment substructures within objects and measure their properties. - Optionally R can be connected to do detailed analysis of results. - Uses MongoDB to manage huge data set.

# Summary VolViewer is used for viewing volume images from, for example, confocal microscopy or optical projection tomography # Features * Real-time volume rendering using an optimized 3D texture slicing algorithm. * Interactive transfer functions to independently adjust opacity and intensity for up to three data channels. * Real-time per channel thresholding, brightness and contrast operators. * On-the-fly gradient computation for local illumination. * Iso-surface computation with surface smoothing. * Section viewing in any orientation / position. * Real-time volume clipping. * 3D measurements, filters & segmentation. * Key frame interpolation for movie export. * Stereo rendering using either quad buffer or anaglyph mode. * Scripting interface to other systems, e.g. Matlab, OMERO, etc. # Project Status * Not supported anymore # Source code * [Source code](https://github.com/ut666/VolViewer "GitHub repository")

ISE-MeshTools is a software designed by Renaud Lebrun, from the university of Montpellier II. ISE-MeshTools is a system for the processing and editing of series of 3D triangular meshes. The system provides a set of tools for editing, positioning, deforming, labelling, measuring and rendering sets of 3D meshes. Features include: • Retrodeformation for un-deforming fossils/deformed specimens • Point and curve primitives for placing the exact type of landmark points you’re interested in • Easy to use 3D interface for positioning and manipulating sets of surfaces and landmark primitives • Mesh tagging, labelling and colouring (to allow for the creation of anatomy atlases) • Mesh scalar computation and colouring (based upon curvature/thickness etc...) Lebrun, R., ISE-MeshTools, a 3D interactive fossil reconstruction freeware., 12th Annual Meeting of EAVP, Torino, Italy ; 06/2014

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.

A Java Package for Geometrical Image Transformation, works up to 5D.

• Affine
• Crop
• Embed
• Matrix
• Mirror
• Rotate
• Scale
• Translate
• Turn

Manual Tracking GUI. Many shortcut keys, and after being experienced, manual tracking can efficiently done. Post-editing capability to delete segments, merge and splitting tracks is quite useful.

An often used Laplacian filter for enhancing signals at object boundaries and dots. It works with XY, XYZ, XYZ-T, XYZ-T-Ch1, XYZT-C1-C2 images. Distributed as a part of ImageJ plugin FeatureJ, and included in Fiji. The second URL above is the link to its Javadoc. (imagescience.feature.Laplacian). A primer for using this class in Jython script is in CMCI Jython/Fiji cookbook: FeatureJ.

Priism is an image processing, analysis and visualisation application for multidimensional light and electron microscopy data. It uses the Image Visualization Environment (IVE) library, which is a closed-source C library with documented C and FORTRAN APIs. Priism/IVE was developed at UCSF, and can be obtained free of charge by sending an email request to the developers. Many of the same processing and analysis functions available in other image processing applications can be found here (cropping, resizing, spatial filters, Fourier transforms, segmentation etc.), and it includes a comprehensive html-based offline manual. The "SoftWoRx" package of GE Healthcare (formerly Applied Precision) was based on Priism/IVE.

Fluorescence spectroscopy by image correlation is a technique that allows analysing and characterizing the different molecular dynamics from a sequence of fluorescence images. Many image correlation techniques have been developed for different applications but in particular to study the mechanisms of cell adhesion during migration. These techniques can be used with most imaging modalities: e.g. fluorescence widefield, confocal microscopy, TIRFM. They allow to obtain information such as the density in molecules, diffusion coefficients, the presence of several populations, or the direction and speed of a movement corresponding to active transport when spatial and temporal correlations are taken into account (STICS: Spatio-Temporal Image Correlation Spectroscopy).

This plugin is based on ICS_tools plugin by Fitz Elliott, available here.

Some bugs have been removed, ROI does not need to be squared, fitting is weighted in order to give more weight to the smaller lags (temporal or spatial)

Exemple of use on sample data [fluorescent beads](http://biii.info/node/2577 "Beads") - Select an ROI, start by ICS to get the right PSF size - Then run TICS and select diffusion, or diffusion plus flow model. Remove the first line (autocorrelation) which corresponds to the noise autocorrelation before fitting.

The workflow consists of firstly identifying spot (which can be also gravity center of cells identified by another method), and then secondly compute trajectories by linking these spots by global optimisation with a cost function. This method is part of the methods evaluated in Chanouard et al (2014) as "method 9" and is described in detail in its supplementary PDF (page 65).

Dependencies

Following plugins are required.

1. JAR to be placed under IJ plugin directory
2. A pdf file with instructions and output description is also available in the zip .
3. MTrackJ : Used for visualization of tracks. Preinstalled in Fiji.
4. Imagescience.jar: This library is used by MTrackJ. Use update site to install this plugin.
5. jama.jar. Preinstalled in Fiji.

##Advantages:

• support blinking (with a parameters allowing it or not)
• fast,
• can be used in batch, some analysis results provided.
• No dynamic model.
• The tracking part is not dependent of ImageJ.

Pitfalls:

• does not support division
• the optimization algorithm used is a simulated annealing, so results can be slightly different between two runs.
• No Dynamic model (so less good results but can be used for a first study of the kind of movements)

##The sample data

The parameters used for this example data Beads, were

1. detection: 150
2. the max distance in pixels: 20
3. max allowed disappearance in frame: 1

HDF5 is a data format for storing extremely large and complex data collections. This Fiji/ImageJ HDF5 plugin saves and loads 2D - 5D datasets with flexible options.

In Fiji, the plugin is downloadable via update site "HDF5".

The software is designed for pathologists. Image analysis protocols are built from graphical user interfaces; there is no need for programming experience or an extensive training program. Cloud and deployed solutions are available. Visiopharm can be employed to develop workflows (apps) for the user. Modular structure with multiple packages: VisiomorphDP™ TissuemorphDP™ Arrayimager™ Tissuealign™ Visiomorph™ Tissuemorph™ Microimager™ Fluoimager™

An easy to use, image analysis software package that enables rapid exploration and interpretation of microscopy data.

Measurement of kymograph generally deals with slanted streaks in kymograph to measure velocity of movements. This is a pretty much manual procedure that needs hands-on work. Kymoquant analyzes kymograph by treating patterns appearing in kymograph as texture: for a specified area in kymograph, it detects the most likely orientation of streaks and outputs this result as velocity. This workflow was created to ease the situation when it is difficult to find major direction of streaks only with eyes.

Rigid registration of time series in 3D. A video tutorial is available (be careful of sounds, the video automatically starts!): [Sample Drift Correction Following 4D Confocal Time-lapse Imaging](http://www.jove.com/video/51086/sample-drift-correction-following-4d-co…)