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.

Manual tracking with TrackMate

Description

Manual tracking using Trackmate plugin (comes with FIji, so no installation required if you are using Fiji). 

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Log3D

Description

The freely available software module below is a 3D LoG filter. It applies a LoG (Laplacian of Gaussian or Mexican Hat) filter to a 2D image or to 3D volume. Here, we have a fast implementation. It is a perfect tool to enhance spots, like spherical particles, in noisy images. This module is easy to tune, only by selecting the standard deviations in X, Y and Z directions.

IJ Macro command example

run("LoG 3D", "sigmax=1 sigmay=1 sigmaz=13 displaykernel=0 volume=1");

Quality metric of 3D SPIM stacks

Description

An ImageJ/Fiji macro which measures quality through two stacks of images assumed to be acquired from two opposite angle of views using gray-level standard deviation.

BM3D denoising

Description

BM3D is a recent denoising method based on the fact that an image has a locally sparse representation in transform domain. This sparsity is enhanced by grouping similar 2D image patches into 3D groups. In this paper we propose an open-source implementation of the method. We discuss the choice of all parameter methods and confirm their actual optimality. The description of the method is rewritten with a a more transparent notation that in the original paper. A final index gives nonetheless the correspondence between the new notation and the original notation.

Spheroid simulator

Description

It simulates a three-dimensional ground-truth that resembles aspects of a biological object like a spheroid. For each simulated view the signal is attenuated, convolved with an effective PSF, and anisotropically sampled using a Poisson process. 

3D confocal noise simulator

Description

This Matlab code simulates the noise of the confocal laser scanning microscope depending on the depth in the image stack (serial sections). Using the stack of binary images, it applies different levels of noise in the signal and background parts of the images to simulate confocal images. This is useful for generating "virtual ground truth" images with known values of sample rotation and distortion. 

Mean shift

Description

Mean shift is a filter which acts as edge preserving filter similarly to non local mean or anisotropic diffusion. 

Mean shift can be used for denoising, segmentation or clustering. Two parameters are to be tuned, a spatial size of a patch and a gray level or color distance on which the algorithm is applied.

 

PHANTAST for FIJI

Description

 

The phase contrast microscopy segmentation toolbox (PHANTAST) is a collection of open-source algorithms and tools for the processing of phase contrast microscopy (PCM) images. It was developed at University College London's department of Biochemical Engineering and CoMPLEX.

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DEFCoN-ImageJ

Description

An ImageJ plugin for DEFCoN, the fluorescence spot counter based on fully convolutional neural networks

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Align slices in stack

Description

Align_slices in stack utilized the template matching function cvMatch_Template to do slice registration(alignment) based on a selected landmark.
This function will try to find the landmark or the most similar image pattern in every slice and translate each slice so that the landmark pattern will be the same position throughout the whole stack. It could be used to fix the drift of a time-lapse image stacks.

Source code: link

Input data: image stack
output data: image stack

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