|Jupyter notebook||Software||10/18/2018 - 10:44|
|NEUBIAS TS1||Training Material||10/17/2018 - 19:50|
|ImageJ/FIJI||Software||10/17/2018 - 19:50|
|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: https://imagej.nih.gov/ij/developer/source/ij/plugin/filter/MaximumFinder.java.html
|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|
SIMPLETRACKER a simple particle tracking algorithm that can deal with gaps.
|10/17/2018 - 17:31|
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|
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:
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 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|
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|
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:
|10/04/2018 - 17:14|
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|
A deep-learning solution for stain color normalization in digital histology images
|09/27/2018 - 10:48|
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|
|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|
|simpleITK||Software||09/09/2018 - 22:49|
|cython||Software||09/09/2018 - 22:49|