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.

IJ-OpenCV

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NeuroMorph

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Microscope autopilot

Description

AutoPilot is the open source project that hosts the general algorithm for fast and robust assessment of local image quality, an automated computational method for image-based mapping of the three-dimensional light-sheet geometry inside a fluorescently labeled biological specimen, and a general algorithm for data-driven optimization of the system state of light-sheet microscopes capable of multi-color imaging with multiple illumination and detection arms.

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Minimum cost Z surface projection

Description

This plugin detects a minimum cost z-surface in a 3D volume. A z surface is a topographic map indicating the altitude z as a function of the position (x,y) in the image. The cost of the surface depends on pixel intensity the surface is going through. This plugin find the z-surface with the lowest intensity in an image.

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Interactive watershed

Description

The interactive Watershed Fiji plugin provides an interactive way to explore local maxima and threshold values while a resulting label map is updated on the fly.

After the user has found a reliable parameter configuration, it is possible to apply the same parameters to other images in a headless mode, for example via ImageJ macro scripting.

Simple-Tracker

Description

SIMPLETRACKER a simple particle tracking algorithm that can deal with gaps.

Tracking , or particle linking, consist in re-building the trajectories of one or several particles as they move along time. Their position is reported at each frame, but their identity is yet unknown: we do not know what particle in one frame corresponding to a particle in the previous frame. Tracking algorithms aim at providing a solution for this problem. 

simpletracker.m is - as the name says - a simple implementation of a tracking algorithm, that can deal with gaps. A gap happens when one particle that was detected in one frame is not detected in the subsequent one. If not dealt with, this generates a track break, or a gap, in the frame where the particle disappear, and a false new track in the frame where it re-appear. 

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@msdanalyzer

Description

Mean square displacement (MSD) analysis is a technique commonly used in colloidal studies and biophysics to determine what is the mode of displacement of particles followed over time. In particular, it can help determine whether the particle is:

  • freely diffusing;
  • transported;
  • bound and limited in its movement.

On top of this, it can also derive an estimate of the parameters of the movement, such as the diffusion coefficient.

@msdanalyzer is a MATLAB per-value class that helps performing this kind of analysis. The user provides several trajectories he measured, and the class can derive meaningful quantities for the determination of the movement modality, assuming that all particles follow the same movement model and sample the same environment.

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Examples of tracks to perform MSD analysis.

FNIRT

Description

Non linear registration intensity based for MRI brain exams. To be applied after FLIRT

a brain mri

FMRIB's Linear Image Registration Tool FLIRT

Description

FLIRT (FMRIB's Linear Image Registration Tool) is a fully automated robust and accurate tool for linear (affine) intra- and inter-modal brain image registration.

FLIRT comes with a main GUI as well as three supporting guis:

  • ApplyXFM - for applying saved transformations and changing FOVs
  • InvertXFM - for inverting saved transformations
  • ConcatXFM - for concatenating saved transformations

StainGAN

Description

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

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