Methods and Techniques Discussion => Image Analysis => Topic started by: arnotts on November 17, 2005, 01:37:27 AM

Title: software ?
Post by: arnotts on November 17, 2005, 01:37:27 AM
I need to count the no. of immunoreactive cells within the sections and also do different meausrements on the sections. Besides printing the photos on paper and counting manually, is there any software available that can do the job?

Title: software ?
Post by: excalibur on November 22, 2005, 08:14:20 PM
Check with some of your local hospitals or clinical labs and see if they will let you use their systems used to count cytology specimens. They may let you use it after hours because of their need to read patient slides.
Title: software ?
Post by: discman on January 06, 2006, 08:35:35 AM

I would recommend ImageJ. It's free available and quite powerful and portable to various systems. In addition you can tailor the proggie to your needs by downloading add-ons and plug-ins.


Title: software ?
Post by: discman on January 06, 2006, 08:57:50 AM
Me again...

Here you'll find a manual to ImageJ:

Title: software
Post by: hokie on May 24, 2006, 09:29:26 AM
You might want to look into Visiopharm as well.  It offers quite a few feature and has a fairly reasonable interface.  Some of these packages have a really high learning curve which can really delay getting started.
Title: Re: software ?
Post by: indra-dr on October 25, 2007, 05:07:39 PM
I use Stereo Investigator.  It is great software with great support. 

Also, if you read many of the top research papers in the field, this is the system that is most widely used.
Title: Re: software ?
Post by: hokie on October 26, 2007, 11:26:43 PM
This simply is not so. I have read well over a thousand of the top research papers and know that CAST is used 10x as often as all other systems combined when it comes to top research papers.

A runner up is unclear since I see so few papers using other systems. It might be either Stereologer or ImageJ. New methods and innovative concepts are pushed through researchers associated with Stereologer and there are plenty of macro writers out there making image processing packages do interesting things. Don't overlook the innovative contributions being made by Howard and reed through ExploraNova.

Title: Re: software ?
Post by: indra-dr on November 10, 2007, 02:48:03 PM
Your claim is a little bizarre and is not one that I concur with based on my personal observations.  I am not sure why you don't acknowledge the simple truth that MBF is used far more widely than the other systems.  Hokie, from your other posts I can see that you may not be "unbiased" in your perceptions since you stated that you used to work for Visiopharm. So, I am guessing that you have a competitive axe to grind.

For the information of others who may read this, I just came back from the Society for Neuroscience meeting where I looked at dozens of posters that used stereology.   From my count of the posters I observed,  over 80 used the Stereo Investgator system.  5 used Stereologer. 7 used CAST (one was by Visiopharm themselves). 

As I have mentioned in one of my other posts here, I am a very happy MBF customer.  Also, I have a number of colleagues who are very pleased with Stereo Investigator. When I visited the MBF booth at SfN, I found that this is common among other users.  I can't recommend the system highly enough. 

FYI, I also visited the Visiopharm, ExploraNova, 3i and Bioquant booths where I received demonstrations of their latest software and spoke with their representatives.  My evaluation is that MBF is by far the best system out there.
Title: Re: software ?
Post by: randy dumouchel on December 13, 2007, 11:23:56 AM
Beware, be very aware about the misinformation sent out on this and other blogs about computerized stereology. In case there's still one or two people who have not figured it out -- messages under the name "indra-dr" are posts from MBF, the company that sells the pathetic StereoInvestigator software. Here's a novel idea -- why don't you spend your time trying to improve your product, which we made the mistake of buying a while back. To everyone else, the good news is that StereoInvestigator hardware can be used with other software packages; if you made the same mistake I did you'll just be out the cost of the StereoInvestigator software. The best advice -- don't waste that money in the first place.

Shame on you Indra-dr!
Title: Re: software ?
Post by: hokie on January 04, 2008, 10:45:33 AM
My personal observations are quite clear. CAST appears in more articles that I read than all other software combined.

I agree with Randy on your origins. I suggest that you have a "competitive axe to grind" and that you have the "bias".

Posters at a single meeting hardly constitute a proper sample, a useful sample, a representative sample, an adequate sample, and really ... hardly a sample by any stretch of the imagination.

I did read two papers recently that did not use CAST. One was well written and well designed. One was so flawed that I was embarrassed for the authors. These 2 papers appeared in a sea of CAST papers.

Get out of your trade booth at the SFN meeting and count posters all you want. I don't care.

I'd prefer it if the moderator would step in here and remove all of the snooty comments from this forum and restore some semblance of decorum.