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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.

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.

The FindFoci plugins allow the identification of peak intensity regions within 2D and 3D images. The algorithm is highly configurable and parameters can be optimised using reference images and then applied to multiple images using the batch mode. Details of the benefits of training an algorithm on multiple images can be found in the FindFoci paper: 2591

Quote: *A GUI-based program which manually detects spots and places them into previously detected meshes. Currently the program runs from MATLAB only. *

Quote: *SpotFinderZ (from now on simply SpotFinder) detects round, usually diffraction-limited spots inside bacterial cells outlined with MicrobeTracker and places them into the meshes structure produced by MicrobeTracker. The program is written in MATLAB and saves the data in the MicrobeTracker format by appending additional fields.*

The Fourier transform of an image produces a representation in frequency space: i.e. separated according to spatial frequency (effectively scale). The 2D amplitude map of the different spatial frequencies is symmetrical, and is commonly displayed with low spatial frequencies (large features) in the centre, highest spatial frequencies (small features) at the edges. Fourier filtering involves suppressing or enhancing features in the Fourier domain before carrying out an inverse Fourier transform to obtain a filtered real-space image.

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.

Implementation of some image correlation spectroscopy tools

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.

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.

The root tools help to efficiently measure the following characteristics of plant roots: the angle of the opening of the whole root the depth to which it goes down the number of roots at multiple depths (for example 30cm, 35cm, ...) the diameters of the roots at multiple depths (for example 30cm, 35cm, ...)

A collection for tracking microtubule dynamics, written in Python.

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™

Count bacterial colonies on agar plates and measure the occupied surfaces. The user has to provide a selection (roi) of the area that will be analyzed. He can than run the segmentation and if necessary correct the results. In a third step he can run the counting and measurement.

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