The Daily Scan

New biomarker method could increase the number of diagnostic tests for cancer

The UCSF press office reports new biomarker method could increase the number of diagnostic tests for cancer:

A team of researchers, including several from UCSF, has demonstrated that a new method for detecting and quantifying protein biomarkers in body fluids may ultimately make it possible to screen multiple biomarkers in hundreds of patient samples, thus ensuring that only the strongest biomarker candidates will advance down the development pipeline.  The researchers have developed a method to increase accuracy in detecting real cancer biomarkers that is highly reproducible across laboratories and a variety of instruments so that cancer can be detected in its earliest stages.

Cool, as the release notes these finding are significant because they potentially allow many more biomarkers to be used for cancer detection and treatment.

chalk tip #20: systematically viewing all of a slide

In tip #19 we talked about tracking where you’ve been while viewing, but did you know?  You can use ImageScope’s Tracker feature to systematically view all of a slide.  Here’s how:

1. Open a digital slide, select View | Tracker, and click the red Record button to start Tracking.  See tip #19 for details.

2. At the right side of the Tracker, there is a green arrow labeled “Next Un-viewed Region”.

Just keep clicking this button and ImageScope will show you the entire slide, view-by-view.

Each time you click the green arrow, ImageScope will take you to the next un-viewed region of the slide, starting at the top of the tissue area and navigating through the slide in a Z-pattern (pretty much the way you would read a book, going across each row and then down to the next one).

As you view regions, the thumbnail will be updated to show you where you’ve been and the location of your current view.

The Tracker will skip “glass” areas and each view slightly overlaps the adjoining views, so you won’t miss anything.

 

If the sample has multiple parts, each section of tissue is navigated completely before moving on to the next section.

 

When all regions of the slide have been viewed, ImageScope will reward you with a little beep.  You’re done :)

This feature is especially useful on TMA slides and others with multiple sections.

Oh, and I should mention, you can hit the Space Bar as an alternative to clicking the green arrow.  Just keep hitting the Space Bar to navigate through the entire slide, view-by-view.  Really cool.

There is more to be said about Tracking but that’s it for today.  Please try it, you’ll like it!

Research Institute Speeds Cancer Research with High-Performance Computing System

A Microsoft case study on Nationwide Children's Hospital reports Research Institute Speeds Cancer Research with High-Performance Computing System.

The Research Informatics Core at Nationwide Children’s Hospital wanted to increase the speed at which it could digitize pathology slides and support researchers through faster computation of data. The organization worked with the Ohio Supercomputer Center (OSC) to deploy the Windows® HPC Server 2008 operating system to support its efforts. The hospital has experienced improved performance and enhanced researcher productivity with the new system.

The case study is accompanied by a cool video which features Aperio's scanning hardware and viewing and management software (albeit unattributed). 

And although you can't tell in the video, under the covers the inherent multiprocessing capabilities of Aperio's Algorithm Framework for image analysis were exploited by the HPC environment. 

We're proud to be a part of the pioneering work of organizations like Nationwide Children's Hospital and Microsoft, especially to "enhance cancer detection and optimize the pathology review process".

Study: Medical imaging increases U.S. life expectancy

HealthImaging.com reports: Study: Medical imaging increases U.S. life expectancy:

Increased utilization of advanced medical imaging has improved the life expectancy of patients in the United States by nearly nine months, according to a study released this month from the National Bureau of Economic Research. 

The study, led by Columbia University economics professor Frank Lichtenberg, PhD, sought to determine the reach and effect of certain variables on U.S. life expectancy from 1991 to 2004: the effect of the quality of medical care, behavioral risk factors (obesity, smoking, AIDS incidence), and other variables (education, income and health insurance coverage) on life expectancy.  In determining the quality of medical care, Lichtenberg evaluated average quality of diagnostic imaging procedures, average quality of practicing physicians and the mean vintage (FDA approval year) of outpatient and inpatient prescription drugs.

Wow, excellent.  And increased adoption of new modalities like digital pathology will increase life expectancy even more...

chalk tip #19: tracking where you've been while viewing

Did you know?  ImageScope lets you track where you’ve been while viewing a digital slide!  This is one of the cooler features in a pretty cool application, and it demos rather well.  Here’s how you use it, and what it does:

1. Open a digital slide (either from within Spectrum, or a local file).
    
2. Select View | Tracker to enable the Tracker toolbar. It looks like this:

   

   {Sub-tip: like all ImageScope tool windows, the Tracker remembers whether it is visible and where you last put it. Feel free to move it to a convenient edge or corner…}

3. Click the red Record button on the Tracker, and poof! you are now recording where you’ve been!

   

   You can click the black Stop button on the Tracker to stop recording at any time. 

You will notice that the thumbnail image has changed into a grayscale image, with all the tissue areas of the slide colored dark gray, and all the glass areas a lighter gray.  The thumbnail is displaying a Map of all the places you’ve viewed on the slide.  It will look something like this:

As you navigate, the gray will be replaced by colored areas representing the portions of the slide which have been viewed, kind of like cleaning dirt from a window.  For example, here’s what the Map will look like after a little panning and zooming:

{Sub-tip: you can make the thumbnail bigger by dragging its lower left corner.}

Each of the colored areas represents an area of the slide which has been viewed.  The intensity of the color is proportional to the zoom at which each area was viewed – the more zoomed in, the brighter the colors.  You can turn off the Tracking Map by un-checking the Map checkbox to display the normal thumbnail:

There is a lot more to be said about Tracking – it is a pretty powerful feature – but that’s it for today.  Please try it, it is even easier to use than to explain :)

Prostate Cancer: From Inoperable to Cancer Free

From the Mayo clinic's Discovery's Edge: Prostate Cancer: From Inoperable to Cancer Free.

Mayo investigators studying immunotherapy for aggressive prostate cancer have found a combination therapy that has dramatically reduced tumor size to make surgery possible. The findings are preliminary — only two cases thus far — but the results are significant for future research.

Cool.  In addition to the innovative therapy involving the immune system, this case highlights the increasingly more common situation where patients get involved in directing their own care.

Brazilian Veterinary Webinars

 

As you know, Aperio is a global company with systems all over the world, including Brazil.  Check out this cool mention on the ABPV (Brazilian Associacion of Veterinary Pathology) site about Aperio's special webinar presentation in Portuguese about the use of digital pathology in the classroom:

LATEST NEWS June 8, 2009 - Aperio's sytems provide equipment that are used to convert glass slides to digital images with 20x, 40x, 83x and 100x of magnification, preserving original image quality (digital slides do not disappear or break), storage and retrieval of files, and providing immediate access to the digital images anywhere, any time, thereby enabling interactive sharing of images.

On June 16 and 17 June the doctors who are working using Aperio's technology are making a presentation free over the internet.  Dr. Yazmin Alcala be talking on June 16 at 13:00 hours and Dr. Ciro Ferreira da Silva of the ICB, USP, is speaking on June 17 at 14:00 (Brazilian time), for the education and interest of Brazilian pathologists and to share how their colleagues are working today with digital pathology from the classroom to the laboratory.

Further information can be obtained by e-mailing Patricia Helcl.

digital pathology art!

Wow, this is amazing...  below are some pictures showing an exposition of ScanScope scans at the Centre François Baclesse.  They're beautiful!  Click each to enlarge...

(Thanks to Paulette Herlin for sharing)

 

 

 

 

 

Digital pathology in Latin American Teaching

I don't blog about Aperio too much, but wanted to share this because it is so cool; digital pathology is increasingly being used in Latin American Teaching applications.

The challenge is that traditional microscope-based teaching methods were inefficient, inconsistent, and costly.  The solution: Spectrum Education™ was employed as an adjunct to traditional teaching methods, thereby making slide sets among students consistent, saving the time required for microscope management, and reducing the expense of microscope maintenance.

The Brazilian Agencia FAPESP showcases Digital Biology (Google translation to English):

The Faculty of the Institute of Biomedical Sciences, USP implemented a teaching methodology that replaces the microscope for visualization of cellular structures with digital computers connected by a network.

Using software that accesses hundreds of scanned digital slides, teachers choose the structures they want to display and - unlike microscopes - all students in the class can see them at the same time, and they can even use a zoom with the ability to zoom in up to 40X.

And here's a Mexican white paper on La FMVZ, pioneer in Mexico in using virtual micropscopy (Google translation to English):

The faculty of veterinary medicine and animal husbandry has developed a virtual microscope that benefits a large number of teachers, researchers and alumni of subjects such as parasitology, pathology and histology.

The program started with a project for "the educational impact of virtual microscopy in the laboratory of veterinary parasitology", which proposes the use of virtual microscopy, a sophisticated digital imaging computer, as complementary tools for teaching laboratories and a communication tool between professionals.

As valuable as digital pathology is in the U.S., it is equally valuable if not more so in other countries which may have fewer pathologists to cover larger areas.

 

chalk tip #18: using ImageScope to measure viewing response time

Today’s chalk tip is one of my favorites.  Did you know you can use ImageScope to measure viewing response time?

ImageScope can randomly access views of a slide and measure how long it takes to retrieve and display them.  Here’s how you can do this:

1. On the Windows taskbar, click Start | Run.


2. Type “imagescope /t” into the Run dialog box, like this:

 

ImageScope will start and open a blank window. You will see that it includes a Testing menu:



3. Open an image from the server for which you want to test viewing response time.  You can do this by signing on to Spectrum, listing or searching for slides, and then clicking on a slide thumbnail.  If you want to test with an Aperio server, you can select a slide from http://www.aperio.com/gallery.


4. Zoom in all the way, e.g. click the 20X button:



5. From the Testing menu, select Timing:



6. In the Timing Interval dialog box enter the number of seconds between each view, then click OK.  Generally the default value of 5 seconds works well, so you can just click OK.



7. The timing test will start!  ImageScope will begin randomly fetching views from the slide at the time interval you’ve specified.  The Elapsed time to retrieve and display each view will be displayed in the lower right corner of the status bar, along with the Average response time (both in seconds).



8. The timing test will continue until you stop it by selecting Timing from the Testing menu again.

A few notes about measuring viewing response time in this way:

• The viewing response time is generally a measure of network bandwidth, not server speed.  It takes a lot of bandwidth and very little computing speed to serve digital slides.
• The bandwidth at the server usually determines the viewing speed, but in some cases it can be the bandwidth at the client.
• The response time depends on the size of the window.  The larger the window, the more data have to be retrieved, transmitted, and displayed for each “view” of the slide.

Cheers and have fun measuring response time!