[Histonet] Image analysis software

[Elizabeth Chlipala]

Judi

Through the years we have used a wide variety of software applications, we have been performing image analysis since 2006, we started whole slide scanning in 2007.  We have used various modules from Zeiss, Image Pro, Aperio's Toolbox, Definiens and free shareware such at Image J.  There are also new vendors on the market such as Indica Labs and Visopharm.  I think you need to make an educated decision based upon what your needs are and how complex your analysis is and the price of the product, some of the commercially available software packages can be expensive.  I saw the earlier post that discussed Image J and that might be a good option to start with if you have the time and ability to learn how to work with the software, you would be surprised to learn that Image J can do quite a bit.  The only thing that it may not be capable of is pattern recognition, others that use the software can comment on that aspect.  I do know that it is easier to trace in Image J than it is in some of the viewer software that are linked to a particular scanner. 

The other software solutions may be a bit easier to understand and work with initially but there will always be a learning curve associated with any software package that you choose to use.  Most software packages will support different file types, such as tiff or modified tiff, you will need to make sure the image format your scanner generates is compatible with the software you choose.   My suggestion would be to look at all of them and determine what is best for your use cases.  I would also be a bit forward thinking, you might think that you only need the software to do certain things but as you use the technology more you will see that you will want to use if for other use cases.  

The other thing I want to comment on is that the success of your image analysis is not just related to the software that you choose to use  but also the quality, consistency and reproducibility of your histology preparations.  

If you want more information on the topic I would suggest going to the DPA - Digital Pathology Association website, it has a list of most of the vendors in the space and if you become of member, its $50.00 for technologists, you will have access to all of the past presentations from the Pathology Visions conferences and webinars.  Here is the link to the website.  The other option is to attend the Pathology Visions conference, it a conference geared towards digital pathology.  If you are a NSH member there is a scholarship available to attend the conference, you could apply for that.  The links to the NSH scholarship and the Pathology Visions conference are below. The list of vendors is under the resources tab.  

https://digitalpathologyassociation.org/

https://digitalpathologyassociation.org/pathology-visions-2016

http://nsh.org/content/digital-pathology-association-scholarship-pathology-vision

Good Luck

Liz

Elizabeth A. Chlipala, BS, HTL(ASCP)QIHC
Premier Laboratory, LLC
PO Box 18592
Boulder, CO 80308
(303) 682-3949 office
(303) 682-9060 fax
(303) 881-0763 cell
liz at premierlab.com
www.premierlab.com

Ship to Address:

Premier Laboratory, LLC
1567 Skyway Drive, Unit E
Longmont, CO 80504


-----Original Message-----
From: Judi Ford via Histonet [mailto:histonet at lists.utsouthwestern.edu] 
Sent: Thursday, February 25, 2016 5:36 PM
To: histonet at lists.utsouthwestern.edu
Subject: [Histonet] Image analysis software

Hi everyone,
We are in the middle of looking at image analysis software and I was wondering what software programs people are using. Why did you pick the one you are using? Are you using it for brightfield whole slide analysis or for fluorescent slide analysis?  What file types can be used with your software?

I would love to hear your experiences.

Thanks,
Judi
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