Java

This small plugin demonstrates the use of OpenSlide in java: it  will extract an imageJ roi drawn from the thumbnail of the whole slide image, or the full image at the desired resolution from an hammatsu NDPI file. Note that z stack are not supported by openslide (neitheir ndpiS).

PSFj is a software tool that automatically analyses the full field-of-view (FOV) performance of a given fluorescence microscope/objective lens combination with respect to its optical resolution and chromatic aberrations. PSFj provides reporting functions to document the momentary performance of a system and it allows for the export of the obtained data, e.g. for image restoration purposes. PSFj is based on ImageJ and JAVA, and runs on Windows, Mac, and Linux PCs as a stand-alone application.

Starting from image stacks, the nuclear boundary as well as nuclear bodies are segmented. As output, NucleusJ automatically measures 15 parameters quantifying shape and size of nuclei as well as intra-nuclear objects and the positioning of the objects within the nuclear volume.

This plugin converts all occurrences of red in a red/green image with magenta, effectively replacing it with a magenta/green merge.

Note: the plugin completely ignores the blue channel, and replaces it with a copy of the red channel.

LBADSA is based on the fitting of the Young-Laplace equation to the image data to measure drops.