Imaris 8.3 – Analysis, Segmentation and Interpretation of 3D and 4D Microscopy datasets

Imaris 8.3

:: DESCRIPTION

Imaris is Bitplane’s core scientific software module for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy datasets.

::DEVELOPER

BITPLANE AG

:: SCREENSHOTS

Imaris

:: REQUIREMENTS

  • Windows/MacOsX

:: DOWNLOAD

 Imaris

:: MORE INFORMATION

OpenSPIM 20150427 – Open-access Light-sheet Microscopy Platform

OpenSPIM 20150427

:: DESCRIPTION

OpenSPIM is an Open Access platform for applying and enhancing Selective Plane Illumination Microscopy (SPIM).

::DEVELOPER

OpenSPIM team

:: SCREENSHOTS

OpenSPIM

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 OpenSPIM

:: MORE INFORMATION

Citation

Nat Methods. 2013 Jul;10(7):598-9. doi: 10.1038/nmeth.2507. Epub 2013 Jun 9.
OpenSPIM: an open-access light-sheet microscopy platform.
Pitrone PG, Schindelin J, Stuyvenberg L, Preibisch S, Weber M, Eliceiri KW, Huisken J, Tomancak P.

FOCAL – Cluster Analysis for Super-Resolved Microscopy

FOCAL

:: DESCRIPTION

FOCAL (Fast Optimized Cluster Algorithm for Localizations) is a rapid density based algorithm for detecting clusters in localization microscopy datasets. FOCAL is easily optimized to reduce artifacts that commonly degrade image reconstructions and minimize the detection of false or pseudo clusters.

::DEVELOPER

Milstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • MatLab

:: DOWNLOAD

 FOCAL

:: MORE INFORMATION

Citation

Fast Optimized Cluster Algorithm for Localizations (FOCAL): A Spatial Cluster Analysis for Super-Resolved Microscopy.
Mazouchi A, Milstein JN.
Bioinformatics. 2015 Nov 4. pii: btv630.

SIMToolbox 1.2 – MATLAB toolbox for Structured Illumination Fluorescence Microscopy

SIMToolbox 1.2

:: DESCRIPTION

SIMToolbox is an open-source, modular set of functions for MATLAB designed for processing data acquired by structured illumination microscopy.

::DEVELOPER

Multimedia Technology Group

:: SCREENSHOTS

SIMToolbox

:: REQUIREMENTS

  • Windows
  • MatLab

:: DOWNLOAD

 SIMToolbox

:: MORE INFORMATION

Citation

SIMToolbox: a MATLAB toolbox for structured illumination fluorescence microscopy.
Křížek P, Lukeš T, Ovesný M, Fliegel K, Hagen GM.
Bioinformatics. 2015 Oct 6. pii: btv576.

imageHTS 1.19.0 – Analysis of high-throughput Microscopy-based Screens

imageHTS 1.19.0

:: DESCRIPTION

imageHTS is an R package dedicated to the analysis of high-throughput microscopy-based screens. The package provides a modular and extensible framework to segment cells, extract quantitative cell features, predict cell types and browse screen data through web interfaces.

::DEVELOPER

Huber Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

  imageHTS

:: MORE INFORMATION

Xmipp 3.1 – X-Windows-based Microscopy Image Processing Package

Xmipp 3.1

:: DESCRIPTION

Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy.

::DEVELOPER

Xmipp Team

:: SCREENSHOTS

:: REQUIREMENTS

  •  Windows with Cygwin /Linux/MacOsX

:: DOWNLOAD

 Xmipp

:: MORE INFORMATION

Citation

C.O.S. Sorzano, R. Marabini, J.M. Carazo, J. Velazquez-Muriel, J.R. Bilbao-Castro, S.H.W. Scheres, J.M. Carazo and A. Pascual-Montano.
XMIPP: A new generation of an open-source image processing package for Electron Microscopy.
J Struct Biol. 2004 Nov;148(2):194-204.

MOSAIC 201305 – ImageJ plugin for Biological Fluorescence Microscopy

MOSAIC 201305

:: DESCRIPTION

MOSAIC (MOdels, Simulations, and Algorithms for Interdisciplinary Computing) , the image-processing algorithms developed at the MOSAIC Group for fluorescence microscopy , are available as plugins for the popular free image processing software ImageJ.

::DEVELOPER

MOSAIC group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MOSAIC

:: MORE INFORMATION

Citation:

I. F. Sbalzarini and P. Koumoutsakos.
Feature Point Tracking and Trajectory Analysis for Video Imaging in Cell Biology,
Journal of Structural Biology 151(2):182-195, 2005.

BioformatsConverter rev3672 – Batch Converting Microscopy Image Formats

BioformatsConverter rev3672

:: DESCRIPTION

BioformatsConverter is useful for batch converting microscopy image formats, like STK, LSM, LIE, ZVI etc etc, to OME-TIFF or PNG files.

::DEVELOPER

Bangham Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • Java

:: DOWNLOAD

 BioformatsConverter

:: MORE INFORMATION

Farsight 0.4.4 – Quantitative Tools for Studying Complex and Dynamic Biological Microenvironments from 4D/5D Microscopy Data

Farsight 0.4.4

:: DESCRIPTION

The goal of the FARSIGHT project is to develop and disseminate a next-generation toolkit of image analysis methods to enable quantitative studies of complex & dynamic tissue microenvironments that are imaged by modern optical microscopes. Examples of such microenvironments include brain tissue, stem cell niches, developing embryonic tissue, immune system components, and tumors. Progress in mapping these microenvironments is much too slow compared to the need. Our knowledge of these systems has been painstakingly “pieced together” from large numbers of fixed, 2-D images of specimens revealing a small fraction of the molecular ‘players’ involved. The goal of this project is to help accelerate progress by: (i) harnessing the power of modern microscopy to help see the microenvironments in a much more detailed, direct, and comprehensive manner; and (ii) computational tools to analyze the multi-dimensional data produced by these microscopes.

::DEVELOPER

Farsight Team

:: SCREENSHOTS

Farsight

:: REQUIREMENTS

  • Windows / MacOSX /Linux

:: DOWNLOAD

 Farsight

:: MORE INFORMATION

Citaition

The FARSIGHT trace editor: an open source tool for 3-D inspection and efficient pattern analysis aided editing of automated neuronal reconstructions.
Luisi J, Narayanaswamy A, Galbreath Z, Roysam B.
Neuroinformatics. 2011 Sep;9(2-3):305-15. doi: 10.1007/s12021-011-9115-0.