Automated

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")