The Daily Scan

Meet the Virtual Dermatopathology Lab

The DarkDaily has an interesting story: Meet the Virtual Dermatopathology Lab, doing business from Boston:

Telepathology, Federal Express, and internet technologies are the cornerstones of a flourishing second opinion business by dermatopathologists in Boston, Massachusetts.  In just a few years, the practice has built a national and international clientele.  This confirms that there is already overseas demand for access to expert pathologists with subspecialty skills.

Another unique twist to this pathology second opinion business is its use of a subscription arrangement.  Referring pathology groups can pay sliding flat fee per case, based on a pre-agreed monthly volume.  This arrangement has proved popular.

I'm sure Dr. Zembowicz and his colleagues are blazing a trail which many others will follow.  And of course, this type of service is greatly facilitated by digital pathology.  Very cool.

岩手医大 澤井先生のスライド (Iwate Medical School Dr. Sawai's Secondary Consultation Video with ScanScope)

I wanted to share the interesting news of an Aperio user in Japan, Dr. Sawai, who has produced a video and published a book on remote consultation using digital pathology in partnership with NTT (Japanese AT&T).  It nicely showcases the Aperio ScanScope CS as you’ll see in the 4 min. video (in Japanese):

http://www.ntt.com/ict/trend/article/future/virtualslide/

In addition to the digital pathology system, he introduces a laboratory information system where users can submit a consultation request to multiple remotely located physicians and receive back diagnosis information from many different angles.  Dr. Sawai is an important champion of digital pathology and it is great to see this kind of adoption taking place all over the world.

what do we call an interpretation made using digital pathology?

Bruce Friedman asks the interesting question, "what do we call an interpretation made using digital pathology"?  He suggests "soft copy read".

My own preference is for "digital read", or perhaps "digital interpretation".  Although I might reserve the latter for situations where a computer application made the interpretation, rather than a human pathologist.

What do you think?  What's the best term for this?

[Update: you may be interested in this further discussion on Bruce's blog]

Please feel free to comment with your thoughts...

follow us on twitter! - aperiotechno

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Jared N. Schwartz, M.D., Ph.D., Joins Aperio as Chief Medical Officer

Just wanted you to know; Aperio has appointed Dr. Jared Schwartz as Aperio’s Chief Medical Officer:

Jared N. Schwartz, M.D., Ph.D., Joins Aperio as Chief Medical Officer

We’re very pleased; many of you know Jared; he’s an experienced and influential pathologist and we’re delighted to have him join us.  As Aperio CEO Dirk Soenksen noted in the press release:

We believe the clinical market is poised for rapid growth, and look forward to working together with Dr. Schwartz to develop and execute strategies for improving laboratory workflow and to identify opportunities for new image analysis tools.

It is going to be great for us to have such an experienced pathologist on staff.

chalk tip #32: fun with the magnifier

For today's tip, we're going to have some fun with the magnifier.

The magnifier is a cool feature of Aperio's ImageScope viewer, a small window drawn over the main window which "magnifies" a region of the image being viewed by 2X:

 
The magnifier always shows the region of the image under the mouse cursor.  As you move the mouse around over the image the magnifier image is updated to match.

The magnifier is toggled on/off with the View | Magnifier command, or by clicking the toolbar icon shown at right.

By default the magnifier is positioned at the lower right of an image, as shown above.  However, the magnifier window may be dragged anywhere you like, like this:

 
If you try this, you'll notice that as you're dragging the magnifier, it magnifies the part of the image it is floating over.  So you can move the magnifier around over the image, just like a magnifying glass. 

Finally, the magnifier window can be resized.  Just position the cursor over the lower right corner, and it will turn into a crosshair; then you can drag the corner to resize the magnifier:

 
After resizing, you can again move the cursor around over the image to magnify different parts of the image.  Or you can drag the resized window over the image to magnify the part of the image it is floating over.

The magnifier is a useful and efficient way to inspect digital slides...  please try it!

Aperio receives Australia-wide coverage as Victorian Biobank ScanScope network commissioned

Aperio received nation wide TV coverage as the state health minister, Daniel Andrews, officially opened the Southern Health hospitals' new ScanScope XT as part of the Victorian Biobank ScanScope network, which is now fully commissioned. The minister referred to the Aperio technology as the "way forward" and one which his government was expecting to further embrace in the future.

Repeat FISH Testing of Breast Tissue Not Cost-Effective for Her-2/neu Determination

Wow this is interesting; Medscape reports Repeat FISH Testing of Breast Tissue Not Cost-Effective for Her-2/neu Determination:

Universal testing of breast cancer tissue for Her-2/neu status with fluorescence in situ hybridization (FISH), as some have proposed, does not increase the identification of candidates for Her-2/neu-directed therapy and is not cost-effective, investigators from Loyola University Medical Center in Maywood, Illinois, announced here at the American Society for Clinical Pathology 2009 Annual Meeting.

There is currently no consensus about Her-2/neu testing on specimen type, the use of multiple-specimen testing (dual testing), or the utility of universal FISH, noted lead author Kelli Ann Hutchens, MD, who is now a dermatopathology fellow at State University of New York in Brooklyn. The senior author of the study was Henry Brown, MD.

Importantly, universal FISH testing did not result in the increased identification of tumors that would potentially be trastuzumab-responsive, they reported. Nor did dual testing of the biopsy and excision specimens with IHC or FISH result in increased identification of Her-2/neu positivity.

This is significant because often labs use IHC as a screening technology, and FISH as the final determinant of Her2 positivity.  This study suggests that IHC can be used as the final determinant, saving the cost (and additional time) of the FISH assay.

Pioneering protein chemist dies

The scientist reports Pioneering protein chemist dies:

Mildred Cohn, a renowned chemist who battled sexual discrimination for much of her career, died last month (October 12) at age 96, succumbing to pneumonia at a hospital in Philadelphia. Combining chemistry, biology, and physics, Cohn opened up new avenues for interdisciplinary biology and helped found the emerging fields of biochemistry and biophysics.

Cohn's research spanned from isotopes to ATP to oxidative phosphorylation. She was one of the first to take meaningful pictures of proteins using nuclear magnetic resonance (NMR), Wand said, and applied this technique to a variety of biochemical problems, such as the mechanisms of enzymes.

Over the course of her career, Cohn was honored with a number of awards, including the National Medal of Science and election to the National Academy of Sciences. She was inducted into the National Women's Hall of Fame the day before she died.

Wow, a real pioneer, in more ways than one, and an inspiration to all of us.  She will be missed.

chalk tip #31: combining multiple images together into one big one

Greetings!  Did you know?  With Aperio's software you can easily combine multiple images together into one big one.

This capability makes use of a file format supported by all Aperio software called an Aperio Compound Image, or ACI.  An ACI is simply a little text file which contains instructions for combining other images together.  ACI files are sometimes made programmatically, but they can also be made "by hand".

Each line in an ACI file specifies the name of an image file, and gives the X and Y coordinates where the image is to be located in a new "compound image".  (By convention, X and Y are measured from the upper left corner, with X going across the image to the right, and Y going down the image to the bottom.)  Each line of an ACI file looks like this:

<image_filename> <Y-offset> <X-offset>

Let's take a simple example.  Suppose we have two images which we want to combine side-by side; here they are shown in the Aperio ImageScope viewer:

madison.svs 58,984 x 35,659

katherine.svs 69,608 x 37,675

(The numbers below each image give their dimensions in pixels.)

To combine these images, let's create a file called paul.aci, which has the following contents:

madison.svs     0     0
katherine.svs   0     58984

Notice that madison.svs is positioned at (0,0), the upper left corner, and katherine.svs is positioned at (58984,0), so that the images will be side-by-side in the compound image.

Now we can open the file paul.aci in the ImageScope viewer, and it looks like this:

  
paul.aci
128,592 x 35,659

Pretty cool!  We can pan and zoom and otherwise view the compound image just as if it was a single file. 

You might notice that katherine.svs is actually a little taller than madison.svs; the default logic is to "trim" the edges.  However this might not be what we want.  Let's change paul.aci just a little, adding a line which says "edgetrim=no", like this:

madison.svs     0     0
katherine.svs   0     58984
edgetrim=no

Now when we open paul.aci in ImageScope, it looks like this:

   
  paul.aci
128,592 x 37,675

No edges were trimmed, and there is now a "gap" at the lower left which is filled with gray.

Let's try a more complicated example, suppose we have two more images (again shown in ImageScope): 

hannah.svs 72,503  x 43,361

samantha.svs 55,848 x 35,307

Let's combine all four of the images above.  We create a new text file named daniel.aci, with the following contents:

madison.svs     0     0
katherine.svs   0     58984
hannah.svs      37675 0
samantha.svs    37675 72503
edgetrim=no

Now if we open the file daniel.aci in the ImageScope viewer, it looks like this: 

daniel.aci
128,592 x 81.036

Magic, huh?  We can pan and zoom through all four images as if they were a single image.  There is no limit to the number of images you can combine in this fashion.  In fact, we used this capability a little while ago to combine 225 digital slides together into an image which was more than one terapixel in size!

There is one more thing I want to mention: you might want to turn a compound image into a single image file.  You can do this with ImageScope!  Just use the Image Extract tool select the entire image, then extract it into a new SVS file.  That might be a good subject for another tip in the future :)

Aperio Compound Images are a powerful capability - please try it!