Posted by
Tim Feinstein-2 on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Image-Processing-Software-tp6821785p6822122.html
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In favor of ImageJ:
* free, designed by and for imaging scientists.
* most basic analytical functions are available as plug-ins and/or incorporated into the (also free) Fiji package.
* difficult to do nonlinear brightness modification (gamma, curves). Most users do not know that this is not an accepted image manipulation in many contexts and can get you in trouble with journals. Gamma/curve adjustment is trivially easy in other apps like Photoshop.
On the minus side:
* Stripped-down user interface. It may take some patience/training for a new user to get the most out of it.
* Advanced techniques like deconvolution and 3D presentation or analysis are best done with proprietary software.
* Many microscope makers package pretty good presentation/analysis software with their system, e.g. Zen for Zeiss, Elements for Nikon. This is often much more user-friendly.
In general I'd say that everyone should have it. The dollar and memory cost are basically nil.
CellProfiler is another free software specifically designed to enable high-throughput image analysis. e.g., automatic segmentation (finding the edge of cells) and measurement of cell area, fluorescence intensity/evenness/object number/size/percent mitotic/apoptotic etc etc etc. I have not used it much but people who do automated siRNA phenotype detection (imaging hundreds of cell micro-colonies on a glass slide, each transfected with a different siRNA) often swear by it.
For deconvolution there are several competing apps, each of which costs quite a bit. I tested Autoquant and Huygens and chose the latter, although Autoquant is also excellent. Both of those also offer quality 3D rendering and analysis, as does Volocity, which I have had a positive experience with in the past.
best of luck,
TF
Timothy Feinstein, PhD
Postdoctoral Fellow
Laboratory for GPCR Biology
Dept. of Pharmacology & Chemical Biology
University of Pittsburgh, School of Medicine
BST W1301, 200 Lothrop St.
Pittsburgh, PA 15261
On Sep 22, 2011, at 5:39 PM, abhijit debroy wrote:
> *****
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http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> *****
>
> Image J is very versatile for most image processing operations. If you would
> want more specific functions like deconvolution etc, look at specific
> softwares (volocity etc.). Image J also has some deconvolution plug ins
> available for free.
>
> Abhijit Deb Roy
> Biomedical Sciences Program
> University of Connecticut Health Centre
> PhD Candidate
>
> On Thu, Sep 22, 2011 at 4:56 PM, Anda Cornea <
[hidden email]> wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>>
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>> *****
>>
>> I absolutely agree.
>>
>> Anda Cornea, Ph.D.
>> Director of the Imaging and Morphology Core
>> Oregon National Primate Research Center
>> 503-690-5293
>>
>>
>> -----Original Message-----
>> From: Confocal Microscopy List [mailto:
[hidden email]]
>> On Behalf Of John Oreopoulos
>> Sent: Thursday, September 22, 2011 1:24 PM
>> To:
[hidden email]
>> Subject: Re: Image Processing Software
>>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>>
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>> *****
>>
>> Try ImageJ. It's free:
>>
>>
http://rsbweb.nih.gov/ij/>>
>> John Oreopoulos
>> Research Assistant
>> Spectral Applied Research
>> Richmond Hill, Ontario
>> Canada
>>
>>
>> On 2011-09-22, at 11:39 AM, Ramshesh, Venkat K wrote:
>>
>>> *****
>>> To join, leave or search the confocal microscopy listserv, go to:
>>>
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>>> *****
>>>
>>> Dear all,
>>>
>>> Our imaging core is looking to buy imaging software for offline image
>> processing, quantification etc. for mostly confocal and multiphoton
>> fluorescence microscopy. I was hoping if folks here had any suggestions or
>> recommendations as to which software to purchase in this regard. Thanks for
>> all your help in advance.
>>>
>>> Best,
>>> Venkat
>>>
>>> Venkat Ramshesh, PhD
>>> Research Instructor/Facility Manager
>>> Department of Pharmaceutical and Biomedical Scinces and Hollings
>>> Cancer Center Drug Discovery Bldg. DD 507
>>> 70 President Street, MSC 140
>>> MUSC, Charleston, SC 29425
>>> Ph: 8438762363
>>> Fax:8438762353
>>> E-mail:
[hidden email]
>>
>
>
>
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