Image correction

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.

Preprocessing step for high-density analysis methods in super resolution localisation microscopy: it aims at correcting artefacts due to these approaches with based on Haar Wavelet Kernel Analysis.

A deep-learning solution for stain color normalization in digital histology images

Estimate the positions and spacing between sections (or at local points) of three dimensional image data. This method may be applied to any imaging modality that acquires 3-dimensional data as a stack of 2-dimensional sections. We provide plugins for both Fiji and TrakEM2.

Acquiarium is for carrying out the common pipeline of many spatial cell studies using fluorescence microscopy. It addresses image capture, raw image correction, image segmentation, quantification of segmented objects and their spatial arrangement, volume rendering, and statistical evaluation. It is focused on quantification of spatial properties of many objects and their mutual spatial relations in a collection of many 3D images. It can be used for analysis of a collection of 2D images or time lapse series of 2D or 3D images as well. It has a modular design and is extensible via plug-ins. It is a stand-alone, easy to install application written in C++ language. The GUI is written using cross-platform wxWidgets library.