昨天在找imagej的tracking的plugin時，意外連到這個pdf檔。覺得內容實在太豐富了，介紹了很多免費的軟體，都是可以用來做生物影像的處理。
這份文件來自Harvard Medical School的Nikon Imaging Center，
資源這麼多，就先轉貼在這裡，等待以後有需要的時候慢慢試試看。
******************************************************************************************
List of Free Software for Microscopy
Compiled by Rainer Heintzmann (King’s College) for the AQLM course, 2009
Data acquisition
Micromanager
http://www.micro‐manager.org/
CamAcqJ (Grant Harris)
Acquisition & Instrument control. Supports QImaging and Luminara cameras and
variable retarders and stages.
http://www.mbl.edu/research/labs/adlc/CamAcqJ/
ScanImage (Vijay Iyer, Karel Swoboda)
Developed for 2photon microscopy and neurobiology/ patch clamping
http://research.janelia.org/wiki/display/ephus/ScanImage
Display and Segmentaton
BioimageXD
3D Visualisation and analysis (nice rendering)
University of Turku & University of Jyväskylä, Finland
Linux/Mac/Windows, VTK + Python based (latest update: 2008‐03‐28)
http://www.bioimagexd.net
VisBio (Curtis Rueden & Abraham Sorber),
3D Visualisation and analysis (nice rendering).
Interfaces with OME. (latest update: 9 Mar 2009),
http://www.loci.wisc.edu/visbio/
V3D (Hanchuan Peng)
Great tools for visualization and segmentation of large (!) datasets.
3D annotation, landmarking, data management,cell segmentation, neuron tracing,
deformable registration, and more (latest update 2009‐May‐5)
http://hanchuan.peng.googlepages.com
Image Processing
COSMOS = COSM Open Souce (Chrysanthe Preza)
… soon to come. Have a look at:, http://cirl.memphis.edu/cosmos
ImageJ: A public domain Java image processing program inspired by NIH Image
for the Macintosh. Windows, Mac OS, Mac OS X and Linux.
Plugins (http://rsb.info.nih.gov/ij/plugins/ ) support various microscopy related
issues. E.g. time‐stamping, resampling, tracking, … LOOK HERE FIRST
http://rsb.info.nih.gov/ij/
DeconvolutionLab (Guillaume Schmit, EPFL)
Toolbox for ImageJ with various deconvolution algorithms. Some of them are state
of the art wavelet based constraints. Only 2^n sized images!
Ask Daniel Sage (daniel.sage@epfl.ch), EPFL if interested in using.
3D_Deconvolution (Pierre Besson, Cédric Vonesch and François Aguet, EPFL)
3D deconvolution package with PSF generation. Only 2^n sized images.
http://bigwww.epfl.ch/demo/deconvolution3D/
Iterative Deconvolve 3D (Bob Dougherty, OptiNav, Inc.)
Memory intensitve.
http://www.optinav.com/imagej.html
DeconvolutionJ (Nick Linnenbrügger)
http://rsb.info.nih.gov/ij/plugins/fftj.html
Voxx: A Volume Rendering Program for 3D Microscopy. Voxx is a voxel‐based (not
surface‐based) 3D rendering program which has been optimized for biological
microscopy. This software permits researchers to perform real‐time rendering of
large microscopy data sets using inexpensive personal computers. We developed it
to explore 3D datasets collected on confocal and multiphoton microscopy systems,
but it can also render other kinds of data (e.g. CT, MRI, etc.).
http://www.nephrology.iupui.edu/imaging/voxx/
NIH image (Mac only): NIH Image is a public domain image processing and
analysis program for the Macintosh.
http://rsb.info.nih.gov/nih‐image/
Cell Profiler (Ann Carpenter, MIT)
Versatile 2D processing platform for high throughput screening applications.
http://www.cellprofiler.org/
IrfanView + IrfanView plugins: Batch conversion (with image processing),
multipage TIF editing, TIFF, AVI, MPEG, DICOM, … (look under “view – Multipage
images”, Extract images from a movie, …
http://www.irfanview.com/
VisBio: VisBio is a biological (3D) visualization tool designed for easy
visualization and analysis of multidimensional image data.
http://www.loci.wisc.edu/visbio/
IVE & Priism (Sedat lab, UCSF)
http://www.msg.ucsf.edu/IVE/index.html
Tracking
Cell Tracker (Hailin Shen, Univ. of Manchester)
Advanced and useful tool for 2D tracking of cells and features. Uses Snakes. Based
on Matlab. (last update 8 June, 2006)
http://dbkgroup.org/celltracker/
utrack (Jaquaman, Danuser)
For experts – powerful linking algorithm in Matlab,
3D is possible. Many Matlab toolboxes are needed.
http://lccb.scripps.edu/content/download.html
Tracking and Ballon Segmentation, 2D (L. Dupuy)
They also can do tracking but do not show it on the website. Worth asking.
Segmentation pluging can be downloaded:
http://www.archiroot.org.uk
3D Tracking
Website was down. But should be good. Windows only. Zebrafish embryogenesis?
http://www.cbi‐platform.net/
View5D: Java Applet, ImageJ plugin, Matlab plugin
The program View5D interactively displays of up to 5 dimensional volumetric
datasets.
Three orthogonal slicing views, 2D and 3D histograms of intensity (scattergrams),
Basic image processing operations (ratioing, ..), Interactive counting and tagging of
entities, Tracking of 3D movements, Multiplicative display of lifetime or ratio
images.
http://www.nanoimaging.de/View5D/
VTK: For programmers only. The Visualization ToolKit (VTK) is an open source,
freely available software system for 3D computer graphics, image processing,
and visualization. More for expert users, who know how to program. Very
powerful and big community!
http://www.vtk.org/
BIRN: Selection of various useful tools for image processing and analysis. Mouse
Brain Atlas, 3D Slicer, LONI Pipeline, Functional MRI, …
http://www.nbirn.net/Resources/Downloads/
OME: Open Microscopy Environment
Data management for biological light microscopy. Image‐based analysis of cellular
dynamics. Image‐based screens of cellular localization or phenotypes.
OME is a database engine which allows a lab to store all microscopy images along
with metadata; keeping track of projects. Some image processing features available.
http://www.openmicroscopy.org/
DIPimage / DIPlib: (Matlab is needed as a platform)
This Matlab toolbox contains a large amount of very useful (often N‐dimensional)
image processing algorithms. DIPimage features its own datatype (dip_image) and
a convenient browser to quickly investigate the results.
Microscopy‐oriented Features are: Automatic Thresholding algorithms, Cross‐
correlation‐based shift determination, Segmentation algorithms (e.g. watershed
transform), Noise‐filtering (e.g. anisotropic diffusion with local structure tensors),
Convolution, Measurements of labeled entities (e.g. Major axis direction) …
http://www.ph.tn.tudelft.nl/DIPlib/
CudaMat (Rainer Heintzmann)
Using NVidia’s GPUs for fast data crunching in Matlab.
Idea: Make it simple: myImage=cuda(myImage);
Only a subset supported at the moment. Datatypes: single and scomplex
Contact me (heintzmann@gmail.com)
minFunc (Mark Schmidt)
Matlab function for general minimization. Lots of methods implemented.
http://www.cs.ubc.ca/schmidtm/Software/minFunc.html
這份文件來自Harvard Medical School的Nikon Imaging Center，
資源這麼多，就先轉貼在這裡，等待以後有需要的時候慢慢試試看。
******************************************************************************************
List of Free Software for Microscopy
Compiled by Rainer Heintzmann (King’s College) for the AQLM course, 2009
Data acquisition
Micromanager
http://www.micro‐manager.org/
CamAcqJ (Grant Harris)
Acquisition & Instrument control. Supports QImaging and Luminara cameras and
variable retarders and stages.
http://www.mbl.edu/research/labs/adlc/CamAcqJ/
ScanImage (Vijay Iyer, Karel Swoboda)
Developed for 2photon microscopy and neurobiology/ patch clamping
http://research.janelia.org/wiki/display/ephus/ScanImage
Display and Segmentaton
BioimageXD
3D Visualisation and analysis (nice rendering)
University of Turku & University of Jyväskylä, Finland
Linux/Mac/Windows, VTK + Python based (latest update: 2008‐03‐28)
http://www.bioimagexd.net
VisBio (Curtis Rueden & Abraham Sorber),
3D Visualisation and analysis (nice rendering).
Interfaces with OME. (latest update: 9 Mar 2009),
http://www.loci.wisc.edu/visbio/
V3D (Hanchuan Peng)
Great tools for visualization and segmentation of large (!) datasets.
3D annotation, landmarking, data management,cell segmentation, neuron tracing,
deformable registration, and more (latest update 2009‐May‐5)
http://hanchuan.peng.googlepages.com
Image Processing
COSMOS = COSM Open Souce (Chrysanthe Preza)
… soon to come. Have a look at:, http://cirl.memphis.edu/cosmos
ImageJ: A public domain Java image processing program inspired by NIH Image
for the Macintosh. Windows, Mac OS, Mac OS X and Linux.
Plugins (http://rsb.info.nih.gov/ij/plugins/ ) support various microscopy related
issues. E.g. time‐stamping, resampling, tracking, … LOOK HERE FIRST
http://rsb.info.nih.gov/ij/
DeconvolutionLab (Guillaume Schmit, EPFL)
Toolbox for ImageJ with various deconvolution algorithms. Some of them are state
of the art wavelet based constraints. Only 2^n sized images!
Ask Daniel Sage (daniel.sage@epfl.ch), EPFL if interested in using.
3D_Deconvolution (Pierre Besson, Cédric Vonesch and François Aguet, EPFL)
3D deconvolution package with PSF generation. Only 2^n sized images.
http://bigwww.epfl.ch/demo/deconvolution3D/
Iterative Deconvolve 3D (Bob Dougherty, OptiNav, Inc.)
Memory intensitve.
http://www.optinav.com/imagej.html
DeconvolutionJ (Nick Linnenbrügger)
http://rsb.info.nih.gov/ij/plugins/fftj.html
Voxx: A Volume Rendering Program for 3D Microscopy. Voxx is a voxel‐based (not
surface‐based) 3D rendering program which has been optimized for biological
microscopy. This software permits researchers to perform real‐time rendering of
large microscopy data sets using inexpensive personal computers. We developed it
to explore 3D datasets collected on confocal and multiphoton microscopy systems,
but it can also render other kinds of data (e.g. CT, MRI, etc.).
http://www.nephrology.iupui.edu/imaging/voxx/
NIH image (Mac only): NIH Image is a public domain image processing and
analysis program for the Macintosh.
http://rsb.info.nih.gov/nih‐image/
Cell Profiler (Ann Carpenter, MIT)
Versatile 2D processing platform for high throughput screening applications.
http://www.cellprofiler.org/
IrfanView + IrfanView plugins: Batch conversion (with image processing),
multipage TIF editing, TIFF, AVI, MPEG, DICOM, … (look under “view – Multipage
images”, Extract images from a movie, …
http://www.irfanview.com/
VisBio: VisBio is a biological (3D) visualization tool designed for easy
visualization and analysis of multidimensional image data.
http://www.loci.wisc.edu/visbio/
IVE & Priism (Sedat lab, UCSF)
http://www.msg.ucsf.edu/IVE/index.html
Tracking
Cell Tracker (Hailin Shen, Univ. of Manchester)
Advanced and useful tool for 2D tracking of cells and features. Uses Snakes. Based
on Matlab. (last update 8 June, 2006)
http://dbkgroup.org/celltracker/
utrack (Jaquaman, Danuser)
For experts – powerful linking algorithm in Matlab,
3D is possible. Many Matlab toolboxes are needed.
http://lccb.scripps.edu/content/download.html
Tracking and Ballon Segmentation, 2D (L. Dupuy)
They also can do tracking but do not show it on the website. Worth asking.
Segmentation pluging can be downloaded:
http://www.archiroot.org.uk
3D Tracking
Website was down. But should be good. Windows only. Zebrafish embryogenesis?
http://www.cbi‐platform.net/
View5D: Java Applet, ImageJ plugin, Matlab plugin
The program View5D interactively displays of up to 5 dimensional volumetric
datasets.
Three orthogonal slicing views, 2D and 3D histograms of intensity (scattergrams),
Basic image processing operations (ratioing, ..), Interactive counting and tagging of
entities, Tracking of 3D movements, Multiplicative display of lifetime or ratio
images.
http://www.nanoimaging.de/View5D/
VTK: For programmers only. The Visualization ToolKit (VTK) is an open source,
freely available software system for 3D computer graphics, image processing,
and visualization. More for expert users, who know how to program. Very
powerful and big community!
http://www.vtk.org/
BIRN: Selection of various useful tools for image processing and analysis. Mouse
Brain Atlas, 3D Slicer, LONI Pipeline, Functional MRI, …
http://www.nbirn.net/Resources/Downloads/
OME: Open Microscopy Environment
Data management for biological light microscopy. Image‐based analysis of cellular
dynamics. Image‐based screens of cellular localization or phenotypes.
OME is a database engine which allows a lab to store all microscopy images along
with metadata; keeping track of projects. Some image processing features available.
http://www.openmicroscopy.org/
DIPimage / DIPlib: (Matlab is needed as a platform)
This Matlab toolbox contains a large amount of very useful (often N‐dimensional)
image processing algorithms. DIPimage features its own datatype (dip_image) and
a convenient browser to quickly investigate the results.
Microscopy‐oriented Features are: Automatic Thresholding algorithms, Cross‐
correlation‐based shift determination, Segmentation algorithms (e.g. watershed
transform), Noise‐filtering (e.g. anisotropic diffusion with local structure tensors),
Convolution, Measurements of labeled entities (e.g. Major axis direction) …
http://www.ph.tn.tudelft.nl/DIPlib/
CudaMat (Rainer Heintzmann)
Using NVidia’s GPUs for fast data crunching in Matlab.
Idea: Make it simple: myImage=cuda(myImage);
Only a subset supported at the moment. Datatypes: single and scomplex
Contact me (heintzmann@gmail.com)
minFunc (Mark Schmidt)
Matlab function for general minimization. Lots of methods implemented.
http://www.cs.ubc.ca/schmidtm/Software/minFunc.html
