Linux

A python package for background and shading correction of optical microscopy images

BaSiCPy is a python package for background and shading correction of optical microscopy images. It is developed based on the Matlab version of BaSiC tool with major improvements in the algorithm.

Colocalization Colormap –an ImageJ Plugin for the Quantification and Visualization of Colocalized Signals

This ImageJ plugin implements the Jaskolski's algorithm (Jaskolski et al. 2005). It creates a pseudo-color map of correlations between pairs of corresponding pixels in two original input images. With it one can quantitativly visualize colocalization.

This plugin is able to stitch an arbitrary collection or grid of images, it does not matter if it is 2d, 3d, 4d or 5d images as long as all images are of the same type. In contrast to the Pairwise Stitching of two images, this plugins will load (and potentially save) the images from/to harddisc.

This toolkit extracts Spherical Textures: Angular projections of 2D or 3D image objects with subsequent spherical harmonics analysis.

From the author summary: "We introduce a novel method to extract quantitative data from microscopy images by precisely measuring the distribution of intensities within objects in both 3D and 2D. This method is easily accessible through the object classification workflow of ilastik, provided the original image is segmented into separate objects. The method is specifically designed to analyze the convex region in objects, focusing on the variation in fluorescence intensity caused by differences in their shapes or patterns."

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The Pairwise Stitching first queries for two input images that you intend to stitch. They can contain rectangular ROIs which limit the search to those areas, however, the full images will be stitched together. Once you selected the input images it will show the actual dialog for the Pairwise Stitching.