Posted by
Vonderheit, Andreas on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Image-Processing-Software-tp6821785p6823639.html
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Dear Venkat,
It totally depends on what you want to do.
There are very nice open source tools around, of course if you also want to do 3D volume rendering and measuring distances or volumes, or trace neurons it is difficult to find a software capable of doing everything.
I totally do not have any commercial interest, I just recently discussed different option in image processing for a grant and I just (more less) copy and paste the information here.
The list is far from being complete, and I am happy to have learned (thanks to Johan) about "endrov", which I did not know before.
Here it is:
We use different types of open source software.
OMERO (
http://www.openmicroscopy.org/site) is our standard Image database for archiving the images and annotating and sharing them.
For simple image processing we are using Fiji (
http://fiji.sc/wiki/index.php/Fiji), an ImageJ derivative, comes with a certain amount of pre-installed plug-ins.
For segmentation and quantitative measurement of phenotypes we are using CellProfiler (
http://www.cellprofiler.org/).
For image analysis of time lapse movies and tracking of individual cells we are using CellCognition (
http://www.cellcognition.org/).
For registration (stitching) we are using XuvTools (
http://www.xuvtools.org/).
In the field of 3D and 4D visualization, rendering and measurement options following software could be used.
V3D by Hanchuan Peng
http://penglab.janelia.org/proj/v3dThis software can do quite a lot, like 3D and 4D visualization, orthoslice, Neurotracing. The rendering is possible, but quite complicated to adjust, since all values have to be set before calculation, and afterwards the values cannot be changed or adjusted. The calculation of the rendering is very slow. Measurement tools are missing. Something important like an undo-button is missing. When we tested the software it crashed several times.
BioImageXD
http://www.bioimagexd.net/index.phpThis software can read the Leica-lif-format. The GUI looks quite similar to Imaris. Volume rendering and creation of orthoslices can be made easily; the visualization is slow and fuzzy. Right now there is no distance, area, and volume measurement tool, but this is on the list for future development. A neurotracing is also not available. This open source software is one of the better ones and as soon as the measurement tools are established a possible alternative to commercial ones.
ImageSurfer
http://imagesurfer.cs.unc.edu/
This software is java-based and even comes with a deconvolution option. The import of image stacks is quite complicated, since no RGB-stacks are allowed and the grayscale images has to have z, time, and channel information. The supported file formats are a little outdated. Once imported, isosurfaces and volumes can be created and coloured. Orthoslices are possible. The measurement of distances between objects in the 3D volume is not possible. Also the creation of a movie while the 3D-volume is turning or orthoslices are enabled is not possible.
ImageJ or Fiji
http://fiji.sc/wiki/index.php/FijiTo visualize a three dimensional image stack one can use for instance the plug-in "ImageJ 3D Viewer", in this viewer the background can be changed and an animation can be recorded. The stack can be shown as volume or as orthoslice. Surface rendering is not possible for single channels. This plug-in is quite powerful and works nicely without crashes. Measurements are not possible.
Here some commercial software:
* Imaris from Bitplane
* Amira from Visage Imaging
* Volocity from Perkin Elmer
* Arivis browser from Arivis
Best regards
Andreas
Dr. Andreas Vonderheit
Head of Core Facility Microscopy
Core Facilities and Technology
Institute of Molecular Biology
www.imb-mainz.de
http://www.imb-mainz.de/core-facilities/microscopy/and use OMERO for image storage
http://www.openmicroscopy.organd why not also have a look at
http://www.endrov.netwhile you are at it. open source image processing is making great strides at the moment; there is no reason to throw money at the commercial offerings. if you have money to spare, you get more for it by improving our open source software!
/Johan
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End of CONFOCALMICROSCOPY Digest - 21 Sep 2011 to 22 Sep 2011 (#2011-34)
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