Image Title Category Type Description Updated
need a thumbnail Jupyter notebook Software 10/18/2018 - 10:44
NEUBIAS TS1 Training Material 10/17/2018 - 19:50
need a thumbnail ImageJ/FIJI Software 10/17/2018 - 19:50
find maxima comparison. Find Maxima (Python) Software Workflow


Maxima finding algorithm recreated from implementation in Fiji(ImageJ)

This is a re-implementation of the java plugin written by Michael Schmid and Wayne Rasband for ImageJ. The original java code source can be found in: 

10/18/2018 - 17:31
Introduction to ImageJ macro language Training Material

In this session, we will cover the basics of ImageJ macro programming using a simple example: how to quantify signal enrichment at the nuclear rim? Trainees will (re)discover how to record actions, plan a workflow and organise their code. This session will alternate presentation of technical points, to be directly applied during practical exercises. The macro will progressively complexify as new notions are taught.

10/17/2018 - 19:50
2D Gaussian fitting macro (Fiji/ImageJ) for multiple signals. Software Workflow

This script includes a rough feature detection and then fine 2D Gaussian algorithm to fit Gaussians within detected regions. This macro is unique because the ImageJ/Fiji curve fitting API only supports 1-D curve. I get around this by linearising the equation. This implementation is for isotropic (spherical) or anistropic (longer in x/y) diagonally covariant Gaussians but not fully covariant Gaussians (anisotropic and rotated). 

10/17/2018 - 19:46
Request for being upgraded to Confirmed Tagger Forum topic

Please ask here if you want to be upgraded to a confirmed tagger. It means that you can also modify other curators' entries.

10/17/2018 - 17:53
need a thumbnail Simple-Tracker Software Component

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. 

10/17/2018 - 17:31
FoCuS-point Software Collection

FoCuS-point is stand-alone software for TCSPC correlation and analysis. FoCuS-point utilizes advanced time-correlated single-photon counting (TCSPC) correlation algorithms along with time-gated filtering and innovative data visualization. The software has been designed to be highly user-friendly and is tailored to handle batches of data with tools designed to process files in bulk. FoCuS-point also includes advanced diffusion curve fitting algorithms which allow the parameters of the correlation functions and thus the kinetics of diffusion to be established quickly and efficiently.

10/18/2018 - 18:43
Examples of tracks to perform MSD analysis. @msdanalyzer Software Component

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.

10/18/2018 - 17:24
FoCuS-scan Software Collection

FoCuS-scan is software for processing and analysis of large-scale scanning fluorescence correlation spectroscopy (FCS) data. FoCuS-scan can correlate data acquired on conventional turn-key confocal systems and in the form of xt image carpets.

10/18/2018 - 17:35
need a thumbnail BioCat Software Collection

Biocat is a java based software that allows to perform image classification or segmentation using machine learning. Several algorithm for the classification are available.

10/08/2018 - 19:56
a brain mri FNIRT Software Component

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

10/04/2018 - 17:19
FMRIB's Linear Image Registration Tool FLIRT Software Component

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
10/04/2018 - 17:14
Acquiarium functionalities diagram acquiarium Software Collection

Acquiarium is open source software (GPL) 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.

10/04/2018 - 11:47
need a thumbnail StainGAN Software Component

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

09/27/2018 - 10:48
need a thumbnail 3D-DAOSTORM Software Component

Stochastic optical reconstruction microscopy (STORM) and related methods achieves sub-diffraction-limit image resolution through sequential activation and localization of individual fluorophores. The analysis of image data from these methods has typically been confined to the sparse activation regime where the density of activated fluorophores is sufficiently low such that there is minimal overlap between the images of adjacent emitters. Recently several methods have been reported for analyzing higher density data, allowing partial overlap between adjacent emitters.

10/19/2018 - 11:47
3B ThreeB 3B Microscopy Analysis Software Software Component

Bayesian analysis of blinking and bleaching, or 3B microscopy, is a method which analyses data in which many overlapping fluorophores undergo bleaching and blinking events, giving the structure at enhanced resolution.

09/21/2018 - 13:52
need a thumbnail simpleITK Software 09/09/2018 - 22:49
need a thumbnail cython Software 09/09/2018 - 22:49