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Performs watershed algotirhm with ij-1.52i.jar. legacy:ij.plugin.filter.EDM("watershed").

The macro will segment nuclei and separate clustered nuclei using a binary watershed. As a result an index-mask image is written for each input image.

Multimodal image registration based on manual selection of matching pairs of landmarks. This image registration workflow is based
on MATLAB’s image processing toolbox using the identification of sites of clathrin-mediated endocytosis by correlative light electron microscopy (CLEM) as an example.

Tracking tools, such as TrackMate, produce tracks and their role stops there. However, tracks are just an intermediate data structure in the workflow. Their subsequent analysis produces the numbers upon which scientific conclusions are made. The track analysis is most often specific to the scientific question to be addressed, and therefore tracking tools remain generic and seldom include specialized analysis modules. Another toolset is required for track analysis; this workflow focuses on using MATLAB.

Five different samples of Drosophila melanogaster Kc167 cells were stained with Hoechst 33342, a DNA stain. The last sample (labeled nodsRNA) is of wild-type cells. Each of the other four samples (labeled 48, 340, Anillin, and mad2) has a different gene knocked down by RNAi.

The sample preparation is described in more detail by [Carpenter et al. (Genome Biology, 2006)(http://genomebiology.biomedcentral.com/articles/10.1186/gb-2006-7-10-r1…)

This workflow presents single-particle tracking in Fiji using Track-Mate, and track motility analysis in MATLAB using @msdanalyzer. 

Roles

This workflow describes a semi-automatic image segmentation procedure for 3D reconstructions of the coronary arterial tree, after which how different morphometric features are automatically extracted, including vessel lumen diameter of the three main coronaries.

CRImage a package to classify cells and calculate tumour cellularity

CRImage provides functionality to process and analyze images, in particular to classify cells in biological images. Furthermore, in the context of tumor images, it provides functionality to calculate tumour cellularity.

CLIJ2 is a GPU-accelerated image processing library for ImageJ/Fiji, Icy, Matlab and Java.

Image correction software for chromatic shifts in fluorescence microscopy

Daybook 2 is the analysis software linked to argoligth slides. It tests the performance of microscopes on various levels: illumination homogeneity, field distortion, lateral resolving power, stage drift, chromatic aberrations, intensity response... It works with various file formats but requires the use of an argolight test slide. 

Assess the performance of the lasers, the objective lenses and other key components required for optimum confocal operation.

The macro generates orthogonal projections from bead images along the lateral and axial dimensions which are displayed using a customized look-up-table to color code intensities. A Gaussian curve is fit to the intensity profile of a fluorescent bead image and full-with-at-half-maximum (FWHM) values are extracted, and listed next to theoretical values for comparison. 

This plugin allows measuring relevant parameters which helps testing, following and comparing microscopes performances. This is achieved by extracting four indicators out of standardized images, acquired from standardized samples: the estimation of the detector sensitivity, the evaluation of the field illumination homogeneity, the system resolution, and finally the characterization of its spectral registration.

In this tutorial video, a coronary arterial tree is used as the demo example to show in detail how the semi-automatic segmentation workflow, Carving from the open-source image analysis software ilastik, can be used. Tips on how and why a preprocessing is done, as well as parameter settings are provided.

Spimagine is a python package to interactively visualize and process time lapsed volumetric data as generated with modern light sheet microscopes (hence the Spim part). The package provides a generic 3D+t data viewer and makes use of GPU acceleration via OpenCL. If provides further an image processor interface for the GPU accelerated denoising and deconvolution methods of gputools.