Image Title Category Type Description Updated
need a thumbnail matplotlib Software 05/27/2018 - 19:47
Manual tracking with TrackMate Software Component

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

05/27/2018 - 17:36
GIMP Software Collection

This is the official website of the GNU Image Manipulation Program (GIMP).

GIMP is a cross-platform image editor available for GNU/Linux, OS X, Windows and more operating systems. It is free software, you can change its source code and distribute your changes.

Whether you are a graphic designer, photographer, illustrator, or scientist, GIMP provides you with sophisticated tools to get your job done. You can further enhance your productivity with GIMP thanks to many customization options and 3rd party plugins.

05/27/2018 - 16:31
Log3D Software Component

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");
05/25/2018 - 19:07
ImagePy Software Collection

This note presents the design of a scalable software package named ImagePy for analysing biological images. Our contribution is concentrated on facilitating extensibility and interoperability of the software through decoupling the data model from the user interface. Especially with assistance from the Python ecosystem, this software framework makes modern computer algorithms easier to be applied in bioimage analysis.

05/25/2018 - 17:30
need a thumbnail Python Software 05/25/2018 - 03:04
need a thumbnail Tracking2.0 Software 05/24/2018 - 03:29
need a thumbnail Jama Software 05/24/2018 - 03:29
need a thumbnail ImageScience.jar Software 05/24/2018 - 03:29
need a thumbnail jMathPlot Software 05/21/2018 - 01:22
Quality metric of 3D SPIM stacks Software Component

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.

05/20/2018 - 21:03
BM3D denoising Software Component

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.

05/20/2018 - 20:52
Spheroid simulator Software Component

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. 

05/20/2018 - 20:09
3D confocal noise simulator Software Component

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. 

05/20/2018 - 19:59
Mean shift Software Component

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.

 

05/20/2018 - 18:28
PHANTAST for FIJI Software Component

 

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.

05/19/2018 - 11:33
DEFCoN-ImageJ Software Component

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

05/18/2018 - 12:26
need a thumbnail MATLAB Curve Fitting Toolbox Software 05/16/2018 - 19:02
need a thumbnail LOCI Bioformats plugin Software 05/15/2018 - 00:32
Align slices in stack Software Component

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

05/09/2018 - 04:04