Automated

Description

automated open-source image acquisition and on-the-fly analysis pipeline (initially developped for analysis of mitotic defects in fission yeast)

Image removed.

 

maars
Description

This filter uses convolution with a Gaussian function for smoothing. Sigma is the radius of decay to exp(-0.5) ~ 61%, i.e. the standard deviation sigma of the Gaussian (this is the same as in Photoshop, but different from earlier versions of ImageJ, where a value 2.5 times as much had to be entered.

Like all ImageJ convolution operations, it assumes that out-of-image pixels have a value equal to the nearest edge pixel. This gives higher weight to edge pixels than pixels inside the image, and higher weight to corner pixels than non-corner pixels at the edge. Thus, when smoothing with very high blur radius, the output will be dominated by the edge pixels and especially the corner pixels (in the extreme case, with a blur radius of e.g. 1e20, the image will be raplaced by the average of the four corner pixels).

For increased speed, except for small blur radii, the lines (rows or columns of the image) are downscaled before convolution and upscaled to their original length thereafter.

has function
Description

Classification of trajectoire: need tracking results as input and will then classify the trajectories as  brownian motion, confined brownian or directed.

has function
thot
Description

Reconstruct big images from overlapping tiled images on a Spark cluster.

The code is based on the Stitching plugin for Fiji https://github.com/fiji/Stitching

SparkStitching
Description

Working version of a simple GUI frontend for CMTK image registration tools in Fiji

need a thumbnail