Survey Deconvolution Resources

Free Software


1.) Deblurring Code from MIT
The deblurring software is available for free to researchers at academic institutions (universities, schools and government research labs). It is also freely available to users in commercial organizations and companies for internal non-commercial purpose. Use in a commercial company for research or evaluation is allowed.
http://people.csail.mit.edu/fergus/deblur_code_form.html

[11/07/07] Application on images with camera shake or motion blur. References:

http://people.csail.mit.edu/fergus/papers/deblur_fergus.pdf

http://people.csail.mit.edu/fergus/research/deblur.html

2.) LSM transmission deblurring for ImageJ

It can also be used in phase contrast microscopy:
http://image.bio.methods.free.fr/lsmtrans.html

ImageJ (http://rsb.info.nih.gov/ij/) is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.1 or later virtual machine. Downloadable distributions are available for Windows, Mac OS, Mac OS X and Linux. The author, Wayne Rasband (wayne@codon.nih.gov), is at the Research Services Branch, National Institute of Mental Health, Bethesda, Maryland, USA.

[11/13/07] Application in LSM (Confocal Laser Scanning Microscopes) and Phase Contrast Microscope. Not directly advised for Brightfield Microscopes. Possible to ask/find out applicability of LSM Deblur plugin to Brightfield.

Licensed Software

1.) AutoDeblur
Widefield, 2-D and Confocal Microscopy
AutoDeblur has a variety of fast and robust deconvolution algorithms, basic visualization tools,

color/multichannel capabilities, and includes the blind deconvolution which eliminates esoteric point-spread measurements.
http://www.p3i.com/deconvol.htm

2.) Scientific Volume Imaging
3-D Volume Imaging
Free Trial
http://www.svi.nl/

3.) Stanford Database
The cost is $900/year
There is a variety of commercial software available to Stanford researchers who are members of the Bioinformatics Facility through the Keyserver Software Program. The Macintosh and PC software available at these links can be copied from our server to local computers. The Keyserver software manager ensures that software is used according to the manufacturers' licensing requirements.

We have software in the following categories

* Sequence Analysis
* Molecular Modeling
* Graphics & Image Analysis
* Database
* Word Processing and Page Layout
* Mathematics/Statistics/Graphing
* Engineering
* Network

4.) Adobe Photoshop

The "Unsharp" Filter

5 - 8.) [Ref: Blog Entry ] Alternatives we considered included IPLab (Scanalytics / BD Biosciences), Imaging Workbench (formerly Axon Instruments, now INDEC BioSystems), Slidebook (Olympus), and (the ridiculously priced) Metamorph (Molecular Devices). This entry also talks about effectiveness of NIS Elements Deconvolution routine.

9.) NIS Elements

Discussion on NIS Elements 2-D Decon at a blog

Nikon NIS Elements AR

June 17, 2006 at 12:37 pm · Filed under Uncategorized

Less impressive than its optics is Nikon’s new NIS Elements (AR 2.10 HF8) imaging software. Obviously a re-branded version of LUCIA from the Czech company Laboratory Imaging Ltd. The software is developped by an excellent and motivated team of programmers and runs very stable and quickly. However, there a still major flaws, such as the lack of an export function for images and movies (yes, you have to use a screen capture tool…) or a faulty measurement function that reports wrong timing information. I am confident that these issues will be fixed in future versions, but Nikon’s efforts to shield its customers from competent technical support are less than helpful. Furthermore, the package is way overpriced and additional ‘modules’ add further significant cost. A real-time deconvolution module (2D RT decon) is marketed as an industry first, but does not really hold up to the promised usefulness - during my tests it merely had the effect of a sharpening filter. Alternatives we considered included IPLab (Scanalytics / BD Biosciences), Imaging Workbench (formerly Axon Instruments, now INDEC BioSystems), Slidebook (Olympus), and (the ridiculously priced) Metamorph (Molecular Devices).

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   Lab Resources » Nikon NIS-Elements AR said,

   December 7, 2006 @ 12:51 pm
   […] The newest release of NIS-Elements (AR 2.30), Nikon’s microscope imaging software, fixed quite a number of problems that existed in the older versions. However, it unfortunately also introduced some new ones. While the Time Measurement function now reports the correct data, it switches units if more than one minute of data is recorded (making importing the data to other software a pain in the neck). The new background measurement function is great - but doesn’t report the area of the probe which renders it almost useless. Customer support is still non-existent. Well maybe some day NIS-Elements will actually become a great product… (see also old entry) […]
   
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   mad.liny said,

   December 20, 2006 @ 1:00 pm
   I’m an NIS-Elements user (formerly a MetaMorph user), and have followed the improvements of the software from the original version 2.1 to the newer 2.3. Support for my software and imaging system is quite good; perhaps it is because of where you live?
   We have been using the Time Measurement functions since the beginning and have been impressed by the addition of background probe - the area is reported for the background probe when the data is exported to a spreadsheet (e.g., Excel (full)). We also like the ability to measure through Z series data now with the same dialog box in v2.3.
   I agree that export of files can be cumbersome, but I also appreciate that the file format of NIS-Elements is quite unique (one of my reasons for using this software) - all dimensions of a multi-dimensional data set are contained as a single file, in full bit-depth, with non-destructive overlays. We find this capability to be quite useful and powerful. Agreeably, in version 2.1 we found export was necessary for analysis in other programs, but in version 2.3 there have been several analysis enhancements, so we no longer need to export. The Object counting function is very comprehensive and easy to use.
   Regarding the 2D real time deconvolution, of course this is a 2D method, looking at only 1 Z plane, so you should not compare it to 3D blind deconvolution - it is not voxel based: only pixel based. Essentially I understand 2DRT to be using a Wiener Filter to sharpen and suppress background noise. It was described to me as a qualitative haze-reduction filter. This is not unlike other systems’ resharpen masks, nearest neighbor filters, etc. The main difference is, this one is done real-time. So, you are correct - it does sharpening, but also in real-time. I think this is an industry first.
   I feel that NIS-Elements is one of the fastest moving software programs with development. Being a MetaMorph user, and using the same outdated functions for over 10 years, it is nice to see a software program on a more rapid development pace. It has a comparable price to other packages and new versions seem to always add significant improvements, so I find it to be a good investment for an acquisition and analysis platform.
   

10.) FoveaPro

Link