A Component is an implementation of certain image processing / analysis algorithms.

Each component alone does not solve a Bioimage Analysis problem.

These problems can be addressed by combining such components into workflows.

MSRC Registration Toolbox

Description

This python toolbox performs registration between 2-D microscopy images from the same tissue section or serial sections in several ways to achieve imaging mass spectrometry (IMS) experimental goals.

This code supports the following works and enables others to perform the workflows outlined in the following works, please cite them if you use this toolbox:

  • Advanced Registration and Analysis of MALDI Imaging Mass Spectrometry Measurements through Autofluorescence Microscopy10.1021/acs.analchem.8b02884

  • Next Generation Histology-directed Imaging Mass Spectrometry Driven by Autofluorescence Microscopy10.1021/acs.analchem.8b02885

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ContourLines

Description

ImageJ/FIJI plugin generating contour lines with equal spacing on top of an image (using overlay).

jSLIC

Description

jSLIC superpixels - is a segmentation method for clustering similar regions - superpixels - in the given image which are usually used for other segmentation techniques. The only two parameters are average (initial) size of each superpixel and rigidity parameter in range (0,1)

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superpixels - ROI

3D Fill holes (mcib3d)

Description

Runs fill holes operation on 3D images.

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ROI Measure

Description

ROI measurement plug-in for Icy.

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Minimum (3D) Filter VIB Protocol

Description

This component convolves the image with minimum filter. Each voxel is set to the minimum value of its neighborhood. The neighborhood is defined by a kernel, which has a diameter of 3 voxels.

has function
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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.

Gaussian Blur 3D (ImageJ)

Description

Performs 3D Gaussian blurring.

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Watershed (ImageJ ij-1.52i)

Description

Performs watershed algotirhm with ij-1.52i.jar. legacy:ij.plugin.filter.EDM("watershed").

has function
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Chromagnon

Description

Image correction software for chromatic shifts in fluorescence microscopy

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