The Daily Scan

A salute to histology wizards working their magic

From the Galveston County Daily News: A salute to histology wizards working their magic:

In the histology laboratory, maintaining the integrity of the specimen is vital. Histology is the study of tissue. The tissue samples all are unique and irreplaceable. If a tissue sample is lost of destroyed, it definitely can have a negative impact on patient care.

If there are problems with a specimen in the clinical laboratories, another tube of blood can be drawn and fluid and other specimen types collected to replace the lost or damaged specimen.

A tissue sample is much more specific and precious. An example would be a biopsy taken to diagnose cancer. That tiny biopsy may be the only tissue that provides a representative sample of the cancer. The histology technician/wizard must ensure that each tiny piece of tissue is handled correctly through the many hands-on procedures required to process the tissue from its original state to a microscopic slide.

...

I salute the histology wizards in our laboratory.

... From Sandy Hinton, who works in Pathology Clinical Services at the University of Texas Medical Branch in Galveston.  One of the most basic tenets of digital pathology is that good slide preparation is essential.  Amen!

chalk tip #38: linking images and annotation regions

Greetings!  Today we will demystify one of ImageScope's coolest and yet least well-known features. That's right, we're going to talk about annotation links.  (dum dum dum)

Did you know?  With annotation links you can create an ordered sequence of digital slide regions for later display.  Perfect for tumor boards, conferences, many education applications, and even pathologist-to-clinician communications.  The linked regions can all be within one slide, or they can span any number of slides.

Pull up a chair, I'm going to give you a couple of examples.  In the first example we'll annotate several regions within an H&E slide and link them into an ordered sequence.

Step 1: Launch ImageScope, and open the digital slide (or simply select the slide from within Spectrum).  Here's our example slide:

 

Step 2: Create a few annotation regions.  First a rectangle labelled "interesting area", then a free-form region (with the Pen tool) labelled "free-form region of interest", and finally an arrow labelled "wow, this is amazing".  This is what the image looks like with the three annotation regions:

 

Step 3: Link the regions in a sequence.  Open the Link Manager with View | Annotation Link Manager or by clicking the icon on the toolbar, it looks like this:

 

The three annotations are listed at left.  Next create links by dragging and dropping an annotation region on top of another one.  First click on "interesting area" and drag it over "free-form region of interest", then drop it.  This creates a link from the rectange to the free-form region.  Next click on "free-form region of interest" and drag it over "wow, this is amazing", then drop it.  This creates a second link from the free-form region to the arrow. 

Clicking on each region in the Link Manager displays the links from (blue) and to (red) the region:

 

 

 

That's it!  We've created three regions and linked them in a sequence.

To use these links, close the Link Manager and use the Next Link and Previous Link icons on the toolbar to move from one annotation region to another.

Okay, that was cool, but do you have time for another example?  Now we're going to link four separate digital slides together in a sequence.  Ready...set...

Step1: Launch ImageScope, and open the digital slides (or simply select the slides from within Spectrum). Here's our example slides:

 

Step 2: Link the slides in a sequence.  Open the Link Manager with View | Annotation Link Manager or by clicking the  icon on the toolbar, it looks like this:

 

The four slides are listed at left.  Next create links by dragging and dropping a slide on top of another one.  Link the first slide to the second, the second to the third, and the third to the fourth.

Clicking on each slide in the Link Manager displays the links from (blue) and to (red) the slide:

 

 

 

 

That's it!  We've linked four slides in a sequence.

To use these links, close the Link Manager and use the Next Link  and Previous Link  icons on the toolbar to move from one slide to another.  You will notice this works even if all the slides have not been opened.  For example, close all the slides except the first one:

 

Now click Next Link on the toolbar and the second slide will be opened and displayed!

 

Similarly, click Next Link again and the third slide will be opened and displayed:

 

And finally click Next Link once more and the fourth slide will be opened:

 

Isn't that cool?  I thought you'd think so.

In addition to linking regions in one slide together, you can link a region in one slide to another region in a second slide.  This is great for preparing a display sequence of regions for presentation in a tumor board.  And you can also link regions to entire slides!  This is useful for annotating a gross image with links to slides made from tissue blocks cut from it.

Please try this yourself; ImageScope's annotation links are easier to create and use than they are to explain!

ASCP 2010 Annual Meeting Digital Pathology Course Offerings

Keith Kaplan points out: "The upcoming ASCP Annual Meeting will feature several sessions discussing Pathology 2.0, digital pathology, including telepathology and image analysis and personalized healthcare.", and notes: "Looks like an excellent faculty for these sessions. The meeting will take place in San Francisco between October 27-31, 2010."  Sessions include:

• A257 Harnessing Web 2.0 to Improve Consultation and Communication
• SP88 Hauling Pathology and Pathologist into the 21st Century – Telepathology and Image Analysis
• SP89 Expanding the Pathologists’ Toolbox in the Era of Personalized Healthcare – Next-Generation Pathology Technology

It is great to see Oncologists working with their Pathologist partners in adopting new technologies like digital pathology and web tools ("Pathology 2.0") to improve patient care.

ASCO/CAP Guideline Recommendations for IHC Testing of ER and PR in Breast Cancer

The ASCO and CAP have jointly published Guideline Recommendations for IHC Testing of ER and PR in Breast Cancer:

Purpose.—To develop a guideline to improve the accuracy of immunohistochemical (IHC) estrogen receptor (ER) and progesterone receptor (PgR) testing in breast cancer and the utility of these receptors as predictive markers.

Methods.—The American Society of Clinical Oncology and the College of American Pathologists convened an international Expert Panel that conducted a systematic review and evaluation of the literature in partnership with Cancer Care Ontario and developed recommendations for optimal IHC ER/PgR testing performance.

Results.—Up to 20% of current IHC determinations of ER and PgR testing worldwide may be inaccurate (false negative or false positive). Most of the issues with testing have occurred because of variation in pre-analytic variables, thresholds for positivity, and interpretation criteria.

Recommendations.—The Panel recommends that ER and PgR status be determined on all invasive breast cancers and breast cancer recurrences. A testing algorithm that relies on accurate, reproducible assay performance is proposed. Elements to reliably reduce assay variation are specified. It is recommended that ER and PgR assays be considered positive if there are at least 1% positive tumor nuclei in the sample on testing in the presence of expected reactivity of internal (normal epithelial elements) and external controls. The absence of benefit from endocrine therapy for women with ER-negative invasive breast cancers has been confirmed in large overviews of randomized clinical trials.

The CAP have also published a list of Frequently Asked Questions about the Breast Predictive Factors, which are available on their website.

It is not unexpected but it is great that the CAP and ASCO are working so closely together on cancer diagnostic guidelines, much as pathologists and oncologists work together to treat patients.

chalk tip #37: making stand-alone DVDs and thumb drives

Greetings y'all!

Today's tip is incredibly useful: did you know?  With Aperio software you can make stand-alone DVDs and thumb drives!  A stand-alone DVD or thumb drive contains one or more digital slides which are viewable on any computer without installing any software.

To do this, you need a software program called DVDGen (earlier versions were called WebGen, and work the same way).  DVDGen is part of Spectrum and also the KickStart product.

How about an example?  I thought you'd never ask...

Let's say I have four digital slides, and I want to make a stand-alone DVD from them:

  

Step 1: create a folder to hold your slides.  I'm calling mine DVD_100.

Step 2: copy the images into this folder.

Step 3: launch DVDGen.  The program displays a dialog which looks like this:

 
Navigate the folder tree on the left to select folder you created with the images.  Make sure "Make CWS from SVS" is checked.  Then click Generate Website.  You will see the following warning message:

This is a true statement!  It can take several minutes to convert each slide.  Next click OK.

DVDGen will display a running dialog as it converts each slide, like this:

  

When all slides have been converted, you will see the message "generation complete".  And a web browser window will be opened with the contents of the DVD, like this:

That's it, we're done!  Clicking any of the thumbnails launches an interactive web browser view of the slide, without installing any software!

My DVD_100 folder is a complete stand-alone way to view my digital slides.  The folder can be burned onto a DVD, or copied to a thumb drive, or posted to a website, or whatever you want!

* Bonus tip: this is also a great way to prepare for tumor boards...

Technology: For Nations That Lack the Expertise, an Automated System for Detecting TB

The NYTimes has an interesting article in their Technology section: For Nations That Lack the Expertise, an Automated System for Detecting TB:

One of the difficulties of diagnosing tuberculosis is that there is no simple blood or urine test. Instead, a laboratory technician must take a sample of sputum coughed up from the lungs, stain it and inspect it under a microscope for the telltale bacteria, which resemble long-grain rice. It takes expertise that is often rare in poor countries.

Guardian Technologies, a Virginia company that was started to help airport X-ray scanners distinguish explosives in luggage from innocuous plastics and liquids, has developed a system that automatically scans microscope slides for the bacillus. The company’s software algorithms can spot distinctive shapes, colors and densities that untrained eyes may miss. In a recent test in South Africa, which has some of the highest TB rates in the world, the technology was 93 percent accurate in detecting the bacillus on microscope slides and had a false positive rate of less than 2 percent, the company said.

Wow, how cool is that?  *This* is the promise of digital pathology, realized.  Searching for AFB on lung slides is painstaking and time-consuming, not to mention error-prone.  Automating this process with image analysis on digitized slides makes so much sense.

The API launches the Journal of Pathology Informatics

[via Bruce Friedman]: The Association of Pathology Informatics have launched an online journal called the Journal of Pathology Informatics.

The Journal of Pathology Informatics (JPI) is an open access peer-reviewed journal dedicated to the advancement of pathology informatics.  This is the official journal of the Association for Pathology Informatics (API).  The journal aims to publish broadly about pathology informatics and freely disseminate all articles worldwide.  This journal is of interest to pathologists, informaticians, academics, researchers, health IT specialists, information officers, IT staff, vendors, and anyone with an interest in informatics.  We encourage submissions from anyone with an interest in the field of pathology informatics.  We publish all types of papers related to pathology informatics including original research articles, technical notes, reviews, viewpoints, commentaries, editorials, book reviews, and correspondence to the editors.  All submissions are subject to peer review by the well-regarded editorial board and by expert referees in appropriate specialties.

Excellent!  They have a Twitter feed (@pathinformatics) but no RSS feed - yet!

Pathology Innovators Use Web 2.0 to Boost Productivity and Create Clinical Value

The Dark Report have published a free special edition white paper: Pathology Innovators Use Web 2.0 to Boost Productivity and Create Clinical Value.

The time to embrace Web 2.0 technologies is now!  While Web 1.0 users simply visited a Web page, Web 2.0 allows users to interact online via blogging, message boards or social networking profiles such as Facebook or to use Web 2.0 tools specifically designed for medical use.

Web 2.0 capabilities are taking advantage of digital pathology and reaping great benefits from it. Instead of having to pack and ship slides, multiple pathologists can view the same image online from different locations, have online discussions about it and pass control back and forth while looking at the same image. Each pathologist can annotate an image in real time. As a result, pathologists employing digital pathology are saving time, increasing their profits, boosting their productivity and garnering big dividends.

Check it out!

Digital Pathology Association Announces Addition of Three Eminent Pathologists to Board of Directors

The Digital Pathology Association have announced the addition of three eminent pathologists to the DPA board:

The new pathologist Board members are:

• Keith J. Kaplan, MD
  Kaplan is a pathologist, most recently at Mayo Clinic, with interests in general surgical pathology, cytology, gastrointestinal pathology, and pathology informatics.  He is a graduate of Northwestern University Feinberg School of Medicine and completed his pathology training at Walter Reed Army Medical Center.  He blogs daily on digital pathology issues at www.tissuepathology.com.
• Sam V. Machotka, D.V.M., Ph.D., D.A.C.V.P. Senior Investigator, Merck & Co.
  Machotka’s current work includes veterinary pathology of pharmaceuticals and bio-pharmaceuticals in safety studies in rodents, dogs, and non-human primates.  He was the lead investigator for the use of digital images in the evaluation of safety studies.  Dr. Machotka received his D.V.M. from Texas A&M University (1969) and his Ph.D. from George Washington University Medical School (1995).  In addition, he holds Diplomate status in the ACVP and ABT. He was previously a clinical veterinarian and pathologist in the US Army Veterinary Corps from 1969-1978 and a Veterinary Pathologist at Hazleton Labs/Covance Labs from 1978-1998.
• Marcial Garcia-Rojo, MD, Pathology Department, Hospital General de Ciudad Real
  Rojo is staff pathologist and coordinator of information systems at Hospital General de Ciudad Real, Ciudad Real, Spain.  His main research areas are medical informatics, immunohistochemistry, and molecular pathology.  He is currently chair of the European project EURO-TELEPATH, Anatomic Telepathology Network, Action IC0604 of the European Cooperation in the field of Scientific and Technical Research (COST).   Dr. Rojo is the medical coordinator of the regional project on digital pathology of the Health Services of Castilla-la Mancha (SESCAM), “Serendipia” project, aimed to create a regional pathology information system and telepathology services connecting fully digitized pathology departments of 15 public hospitals in Castilla-La Mancha.

Wow, congratulations to the DPA for adding such distinguished members of the pathology community to their board.  And thank you to the new board members for their participation in this important organization.  Among other things, the DPA will run the 2010 Pathology Visions conference.