Ensemble of blocks that implement SODA method for confocal and super-resolution microscopy, in 2 and 3 dimensions
|01/15/2019 - 18:12|
There are many methods in bio-imaging that can be parametrized. This gives more flexibility
|01/11/2019 - 15:39|
AssayScope is an intuitive application dedicated to large scale image processing and data analysis. It is meant for histology, cell culture (2D, 3D, 2D+t) and phenotypic analysis.
|01/09/2019 - 12:36|
|Python 3.6||Software||01/02/2019 - 18:15|
|The Allen Cell Structure Segmenter||Software||Collection||
The Allen Cell Structure Segmenter is a Python-based open source toolkit developed at the Allen Institute for Cell Science for 3D segmentation of intracellular structures in fluorescence microscope images.
It consists of two complementary elements:
|01/02/2019 - 18:15|
The successor of DeconvolutionLab
|12/20/2018 - 19:13|
|EBImage||Software||12/19/2018 - 00:16|
GaussFit_OnSpot is an ImageJ plugin for fitting Gaussian profiles onto selected positions in diffraction-limited images (e.g. single molecules, protein clusters, vesicles, or stars).
The plugin performs a function fit in regions of interest (ROI) around spots marked by point selections in grayscale images. Single or multiple spots can be either selected manually with the Multi-point tool or automatically with the Find Maxima function.
|12/19/2018 - 00:11|
|Spots colocalization (ComDet)||Software||Collection||
Quote " finding and/or analyzing colocalization of bright intensity spots (cells, particles, vesicles, comets, dots, etc) in images with heterogeneous background (microscopy, astronomy, engineering, etc). "
Uses Gaussian-Mexican hat convolution for preprocessing.
|12/17/2018 - 01:49|
|https://www.youtube.com/watch?v=1rC8iAk6-3g||Training Material||12/17/2018 - 01:21|
"PTA2 is an ImageJ1.x plugins that enable automatic particle tracking"
This plugin is developed specifically for single-molecule imaging, so it's good at tracking spots with noisy background.
|12/13/2018 - 00:46|
"The Microscope Image Analysis Toolbox MiToBo is an extension for the widely used image processing application ImageJ and its new release ImageJ 2.0.
|12/11/2018 - 02:09|
h-Dome transformation, useful for spot detection.
Jython code example:
|12/11/2018 - 02:00|
Nessys: Nuclear Envelope Segmentation System
Nessys is a software written in Java for the automated identification of cell nuclei in biological images (3D + time). It is designed to perform well in complex samples, i.e when cells are particularly crowded and heterogeneous such as in embryos or in 3D cell cultures. Nessys is also fast and will work on large images which do not fit in memory.
|12/11/2018 - 01:58|
|http://www.sci.utah.edu/software/fluorender.html||Training Material||12/09/2018 - 19:55|
FluoRender is an interactive rendering tool for confocal microscopy data visualization. It combines the rendering of multi-channel volume data and polygon mesh data, where the properties of each dataset can be adjusted independently and quickly. The tool is designed especially for neurobiologists, allowing them to better visualize confocal data from fluorescently-stained brains, but it is also useful for other biological samples.
|12/09/2018 - 19:55|
3Dscript is a plugin for Fiji/ImageJ for creating 3D and 4D animations of microscope data. In contrast to existing 3D visualization packages, animations are not keyframe-based, but are described by a natural language-based syntax.
|12/11/2018 - 02:10|
Labkit is an open-source tool to segment truly large image data using sparse training data. It has an intuitive and responsive user interface based on Big Data Viewer, allowing users to conveniently browse and annotate even terabyte sized image volumes.
Update site: Labkit
|12/09/2018 - 19:35|
|SciView||Software||Component||12/09/2018 - 19:20|
|https://bitbucket.org/rhenriqueslab/nanoj-squirrel/downloads/||Training Material||12/09/2018 - 19:03|