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Author Topic: Quantitative Image Analysis Systems - Any recommendations?  (Read 11431 times)

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Offline njcragg

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Quantitative Image Analysis Systems - Any recommendations?
« on: January 27, 2006, 04:07:40 AM »
Hi All,

Has anyone got any recommendations and/or advice on image analysis systems?  We are looking to buy a new image analysis system to quantify IHC and perform histometric measurements (although this may require a second system).  Does anyone have a system they can recommend?  Or has anyone looked into this field and can offer any advice.  Up to now, we've looked into Chromavision, Zeiss & Ariol.  

Thanks in advance,

Nicola Cragg
EpiStem Ltd.
Manchester, UK
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Quantitative Image Analysis Systems - Any recommendations?
« on: January 27, 2006, 04:07:40 AM »

Offline Linesider

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Quantitative Image Analysis Systems - Any recommendations?
« Reply #1 on: January 27, 2006, 11:43:38 AM »
We have been using the ACIS II for several years now to scan high resolution images that we then import into metamorph for quantitiative measurements.
We have produced high res virtual slides by lifting the images as tiff files, and producing data not previously possible.  There are some slight seam issues, but it has not affected the data dramatically.
there are also image size issues, one image 0.3 GB, but with the proper processors it is becoming easier to manage/analyze.
Are the applications for clinical or research?
bw

Offline ImmunoNYC

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Re: Quantitative Image Analysis Systems - Any recommendation
« Reply #2 on: January 30, 2006, 11:17:29 PM »
Hi Nicola .... I would love to hear your opinions on what you have tried? Is this for clinical or research? I used the ACIS myself a few years back in research and it was VERY ill suited to research at the time.[/color]

Quote from: "njcragg"
Has anyone got any recommendations and/or advice on image analysis systems?  We are looking to buy a new image analysis system to quantify IHC and perform histometric measurements (although this may require a second system).  Does anyone have a system they can recommend?  Or has anyone looked into this field and can offer any advice.  Up to now, we've looked into Chromavision, Zeiss & Ariol.

Offline njcragg

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IHC Image Analysis
« Reply #3 on: February 07, 2006, 09:32:44 AM »
Hi,

Sorry for the delay, just found the replies!  I can't say that I have a list of pros & cons for each system, as it becomes a very complex area. All the the systems appear to do the basics of what we want and so it's been difficult to understand the differences and make a preference over one than the other.  Also, I don't think you learn the real advantages and limitations of a system until you beginning working with it!

However, we are in the business of contract research and subsequently, we work with a range of different samples from human clinical samples to experimental animal tissues, which ultimately require different types of analysis.  Initially we required a system to quantify IHC, to replace our old system (which calculates optical density of nuclear staining), but we also wanted a system which could perform quantification on other types of staining (nuclear, cytoplasmic, diffuse) and a variety of histometric measurements.  Basically, we need a system with a lot of scope.  

The ARIOL system is set up to do all of the IHC stuff and the company are prepared to write software for the other histometric work, plus there is the flexibility to add to the sytem at a later date, e.g. by adding fluorescence.  The Zeiss system is also modular in this way and could do many of the things we required, in particular the image processing (i.e. after acquisition and before analysis) was very good, although some of the different types of analysis were probably less straightforward to perform.  The Chromavision is less flexible, particularly for our needs and would be more suited to high throughput, routine image analysis.

In saying all this, I would like to emphasize that it is only my opinion based on our needs and I am no way an expert on image analysis.  I think the demos have been very useful for getting a feel about the systems.  When we finally make our purchase and put our new system in place I will probably be able to comment more.

Nicola
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Offline Linesider

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Quantitative Image Analysis Systems - Any recommendations?
« Reply #4 on: February 13, 2006, 10:57:09 AM »
Does the Aperol system allow for large images to be exported??
Do you know what image analysis system they incorporate?
I have been using the ACIS II, but have started looking inot the aperol for resolution issues associated with the ACIS.


Offline hokie

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Re: Quantitative Image Analysis Systems - Any recommendations?
« Reply #6 on: March 07, 2007, 08:00:16 AM »
There are some basic systems out there that provide image processing capabilities such as Image-Pro. I have looked over their manual, but not used their product.

Higher end systems that can do image analysis are more useful. The difference is a person pushing a slider aback and forth to get it "just right" and the computer being "taught" how to separate the image into different components. I have use VIS by Visiopharm and I used to call it magic. A rough breakdown of any picture can be done by asking the system to find, say 4 or 5, different things in the image. It does it.

If you have the funds I would advocate the use of a higher end system such as VIS. In the long run it will save a tremendous amount of time and therefore money. You get so much more out of your time and the equipment that the savings are obvious.
Do more, less well. ~Ewald Weibel

Offline ImmunoNYC

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Re: Quantitative Image Analysis Systems - Any recommendations?
« Reply #7 on: March 07, 2007, 11:59:22 PM »
You say you "used" to call it magic, does this mean you don't think it's magic anymore? If not, why so? What system do you currently use and for what purpose?

Offline hokie

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Re: Quantitative Image Analysis Systems - Any recommendations?
« Reply #8 on: March 08, 2007, 11:01:17 AM »
I used to work for the firm and was always astonished at how well the software worked aand how easy it was to use. I do not work for Visiopharm anymore so I say, "I used to call it magic."

My understanding is that the software is built on some really high end probability engines. let me try to make that a little more understandable.

When a slider is moved to do thresholding there is a simple rule that decides whether or not to made the pixel black or white. One color means it is something I am interested in and the other color means that it is not something I am interested in. The decision is based on the brightness of the pixel either in red, green, or blue, or a combination of the 3 - an overall brightness.

That isn't very useful for most images I have had to deal with. Instead of assigning a simple yes/no, it is/is not, or other binary answer a probability engine assigns a chance that the pixel is one of many possibilities. Suppose that the image is from a section through a joint. Then the image contains all sorts of interesting components: cartilage, bone, marrow, muscle, etc. Instead of trying to pick out each of these one at a time it makes much more sense to try and separate out each of the components in one try. Right? If something is identified as bone, then it can't be cartilage or muscle.

A probability engine begins by assigning probabilities that a pixel is part of bone or cartilage or muscle. This cannot always be done by checking the red, green, blue, and combined values. It might require ratios of these settings. It might require examining whether or not the pixel is a part of a blob, or a long structure, or is near an edge, or any one of many features. The color information plus the spatial information plus other things makes it possible to separate out parts of images that would otherwise be nearly impossible for a computer to do.

I have had the opportunity to use a number of systems from general packages to more specific packages here at Virginia Tech. Currently I am not using an image processing package. I am involved in the reverse process, which is the generation of synthetic images based on geometrical input. The goal of this work is to generate image stacks that can be used to test the ability of humans to correctly apply some stereological procedures.

Like I said, I don't work with Visiopharm anymore, but it is really amazing image analysis software that is worth a look-see by anyone that needs to process images. It's fast and easy to use.
Do more, less well. ~Ewald Weibel

Re: Quantitative Image Analysis Systems - Any recommendations?
« Reply #8 on: March 08, 2007, 11:01:17 AM »