Image correction is the removal of aberrations originating from the imaging instrument, lighting, or sample.

Synonyms
Instrument aberration correction
Image pre-processing
Image preprocessing

Replace Red with Magenta

Description

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.

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HAWK

Description

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.

StainGAN

Description

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

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Z-spacing correction for Fiji

Description

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.

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Aquiarium

Description

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.

Functionalities

Manual Frame Drift Registration

Description

An ImageJ macro for correcting frame drift occurred during image acquisition.

It often happens that you have an image sequence that shows problematic drifting of image frame and at the same time you have some landmarks that could be used for correcting the drift. This ImageJ macro allows you to Manually track the landmark using ImageJ Manual Tracking Plugin. Using the coordinates recorded in the Result window, each frame is shifted back so that the landmark stays in a single place.

Background Subtractor

Description

Histogram-based background subtractor for ImageJ.

The implemented algorithm is based on the assumption that, compared to the background region, object (foreground) regions are small. The plugin builds local histograms and assumes the most occuring intensity to be part of the background.

EnhanceEdges

Description

EnhanceEdges enhances or identifies edges in an image, which can improve object identification or other downstream image processing.

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Retinex

Description

Retinex filtering is based on Land's theory of image perception, proposed to explain the perceived colour constancy of objects under varying illumination conditions. Several approaches exist to implement the retinex principles, among these the multiscale retinex with colour restoration algorithm (MSRCR) combines colour constancy with local contrast enhancement so images are rendered similarly to how human vision is believed to operate.

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Bleach Correction

Description

Three different methods for correcting fluorescence bleaching. 1. Simple (framewise ratio based) 2. Exponential (curve fitting with exponential decay model) 3. Histogram matching (register histogram shape. with 16 bit, it takes long time... it should be improved).

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