Digital Pathology Blog

Happy Thanksgiving

Posts to resume December 1.

Processing Speech and Voice

In everyday life, we automatically and effortlessly decode speech into language independently of who speaks. Similarly, we recognize a speaker's voice independently of what he says. Formisano et al from a recent Science paper show that it is possible to decode the contents of speech and the identity of the speaker from measurements of the brain activity of a listener. They map and decode, trial-by-trial, the spatially distributed activation patterns evoked by listening to different vowels or speakers evoke in distinct patches of the listeners' auditory cortex. The pattern associated with a vowel does not change if the vowel is spoken by another speaker and the pattern associated with a speaker does not depend on what the person says:

"Who" Is Saying "What"? Brain-Based Decoding of Human Voice and Speech

Elia Formisano, Federico De Martino, Milene Bonte, Rainer Goebel

  Can we decipher speech content ("what" is being said) and speaker identity ("who" is saying it) from observations of brain activity of a listener? Here, we combine functional magnetic resonance imaging with a data-mining algorithm and retrieve what and whom a person is listening to from the neural fingerprints that speech and voice signals elicit in the listener's auditory cortex. These cortical fingerprints are spatially distributed and insensitive to acoustic variations of the input so as to permit the brain-based recognition of learned speech from unknown speakers and of learned voices from previously unheard utterances. Our findings unravel the detailed cortical layout and computational properties of the neural populations at the basis of human speech recognition and speaker identification.

Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, University of Maastricht, 6200 MD Maastricht, Netherlands. E-mail: e.formisano@psychology.unimaas.nl

Virtual 3D Microscopy Using Multiplane Whole Slide Images in Diagnostic Pathology

From American Journal of Clinical Pathology

To reproduce focusing in virtual microscopy, it is necessary to construct 3-dimensional (3D) virtual slides composed of whole slide images with different focuses. As focusing is frequently used for the assessment of Helicobacter pylori colonization in diagnostic pathology, we prepared virtual 3D slides with up to 9 focus planes from 144 gastric biopsy specimens with or without H pylori gastritis. The biopsy specimens were diagnosed in a blinded manner by 3 pathologists according to the updated Sydney classification using conventional microscopy, virtual microscopy with a single focus plane, and virtual 3D microscopy with 5 and 9 focus planes enabling virtual focusing.

Regarding the classification of H pylori, we found a positive correlation between the number of focus planes used in virtual microscopy and the number of correct diagnoses as determined by conventional microscopy.

Concerning H pylori positivity, the specificity and sensitivity of virtual 3D microscopy using virtual slides with 9 focus planes achieved a minimum of 0.95 each, which was approximately the same as in conventional microscopy. We consider virtual 3D microscopy appropriate for primary diagnosis of H pylori gastritis and equivalent to conventional microscopy.

Caltech Researchers Use Electron Cryotomography to Get First 3-D Glimpse of Bacterial Cell-Wall Architecture

The bacterial cell wall that is the target of potent antibiotics such as penicillin is actually made up of a thin single layer of carbohydrate chains, linked together by peptides, which wrap around the bacterium like a belt around a person, according to research conducted by scientists at the California Institute of Technology (Caltech).

These findings represent important advances in both biology and imaging technology.  The authors of a study to be published in the Proceedings of the National Academy of Sciences (PNAS) have made available to me their manuscript and the images in the publication.

This first-ever glimpse of the cell-wall structure in three dimensions was made possible by new high-tech microscopy techniques that enabled the scientists to visualize these biological structures at nanometer scales.

"This is both a technological and biological advance," says Grant Jensen, associate professor of biology at Caltech, a Howard Hughes Medical Institute investigator, and the principal investigator on the study.

Here is one image that will not be included in the publication itself that illustrates the cell wall structure and one of the 3D reconstruction.  Look for the full article in PNAS online early edition very soon.

 

Blogging and pathology articles about blogs

Since starting this blog over a year ago I have relied upon "word of blog" from other physician bloggers (see: New Digital Pathology Blog by Keith Kaplan & The Bits and Bytes of Pathology), other digital pathology blogs (see: Medicine 2.0 at the digital pathology blog), online Medicine 2.0 conferences, blogs about blogs and talks at conferences and meetings (see: Medicine 2.0 Congress & Pathology Visions) to tell people about the blog. 

It recently occurred to me through a few calls and e-mails that some frequent readers did not know who was writing these articles so I added an "About" link on the sidebar.  In particular, for physician bloggers, doing so "anonymously" or without professional reference is not good blogging practice as I have written about.

It's perilous to generalize, but the typical academic blog entry comments on - and links to - a news article or an entry on someone else's blog. Most authors of academic blogs allow their readers to post short comments of their own.

A couple of months ago, I came across 2 articles in a pathology journal that commented on blogging and Web 2.0 in pathology, not the other way around. 

So, here is a blog post that comments on articles about blogging and Pathology 2.0.  I think that completes the loop...

Both articles appeared in the September issue of Advances in Anatomic Pathology.  One article entitled "The Blog Phenomenon Hits Pathology" by Dr. Brian Moore of Memorial Medical Center in Springfield, IL who blogs at Neuropathology blog writes:

"Pathology has not been immune to the allure of the blog, and has served as a creative and interactive outlet for pathologists around the world." 

Brian, Bruce Friedman, Jules Berman and a group of pathology residents and myself are among the pathologists and pathologists-to-be who blog.  Brian's comments are right on and I am sure the others in this small group feel the same way.

The strongest case for academic blogging is the freedom of tone. It also offers speed; the opportunity to interact with diverse audiences both inside and outside academe; and the freedom to adopt a persona less rigid than other forms of academic publishing or presentation.

Dr. Darren Wheeler of Quest Diagnostics wrote another article entitled "Online Slide Presentations".  Darren has written several similar articles in the same journal in addition to other publications related to his interests in gynecologic pathology.  Of www.slideworld.org, he writes:

"The freely available slide presentations, maintaining acknowledgement of authorship, also serves as a venue for promoting various institutions and practices." He includes the below screenshot in the article. 

While some of my colleagues here disagree with sites such as these and contributing to them (I have since added several more since Darren's submission), I think his comments again are right on.  What he is really touching on is the simplicity by which these Web 2.0 tools can be used and the impact your contributions to them can have outside one's own institution.  Again, like a blog, viewers can add comments or rate the presentations & share the content you post.

There is also no doubt that academic blogs and content sharing sites will provide a model for academic institutions and societies to externalize and share more of their content and expertise outside of their own centers and organizations and further distribute their own opinions & educational resources. 

I discussed this previously about my own institution's blog and YouTube channel as examples of this.

Researchers aim to learn how patients react to information culled from genome scans

In the Los Angeles Times (11/12) Booster Shots Blog, Rosie Mestel asked what individuals should do with the info they receive after spending "a thou' or two" to learn about their "genetic predisposition to Alzheimer's disease, colon cancer, heart disease, [and] more." Zeroing in on that question, researchers at the Scripps Translational Science Institute are planning to find an answer "with the help of 10,000 employees, family members, and friends of Scripps Health, a nonprofit healthcare delivery network in the San Diego area." Participants will "get a discounted scan of their genome from Navigenics," and "as new data roll in on other genetic links to diseases, those will be added to the database." Then, patients "will in a sense serve as their own controls: They'll be assessed for their mood, habits, and the medical care they seek both before and after they get the scan information." Meanwhile, Mestel pointed out an "interesting fact: Adopted people have been especially keen to enroll in the study."

Mark your Calendar - APIII 2009 - September 20-24, Pittsburgh, PA

 

http://apii.upmc.edu

Mark Your Calendar /  Plan to Attend APIII 2009

Sunday, September 20 –  Thursday, September 24, 2009

Marriott City Center Hotel,

Pittsburgh

Pennsylvania

API Scholarships for Medical Technology Students Announced

The American Proficiency Institute (API) recently announced a new $10,000 scholarship program for medical technology students.   In introducing the program, Dan Edson, API President, explained, "We are looking for future, visionary leaders of the profession. Because of the nationwide shortage of medical technologists, we hope these scholarships will promote the field for future laboratorians."  Junior- and senior-level medical technology students are encouraged to apply. 
Visit www.api-pt.com.

Aperio Receives Second FDA Clearance for Diagnosis of Digital Breast Cancer Slides

Aperio has recently received FDA clearance for interpretation of progesterone receptor to its already approved HER2 clearance for digital reads as well as image analysis applications for ER and PR.

Excellent news for signing out breast cancers with whole slide images on a computer monitor. 

The recent press release states: "Aperio has received its second FDA clearance from the U.S. Food and Drug Administration (FDA) for reading digital PR (Progesterone Receptor) slides from a computer monitor using its patented ScanScope® digital slide scanning system. Aperio previously received FDA clearance for the reading of digital HER2 slides from a computer monitor in December 2007.

The ScanScope System is intended for use as an aid to the pathologist in the detection and quantitative measurement of PR (Progesterone Receptor) by manual examination of the digital slide of formalin-fixed, paraffin-embedded normal and neoplastic tissue immunohistochemically stained for PR on a computer monitor. It is indicated for use as an aid in the management, prognosis, and prediction of therapy outcomes of breast cancer."

 Full press release

Nikon Instruments Partners With ChromoDynamics To Bring Hyperspectral Imaging to Widefield Microscopy

There is no doubt that hyperspectral imaging technologies will play a role in diagnostic surgical pathology for the reasons I already discussed and recently blogged about (see: Top 10 Medical Innovations for 2009).  Nikon has recently entered the market with this recent press release:

 

"Nikon Instruments, Inc. ( www.nikoninstruments.com) and ChromoDynamics, Inc. ( www.chromodynamics.net) have announced a valued-added reseller agreement enabling Nikon to deliver ChromoDynamics' new HSi-300 system, providing high-performance, widefield hyperspectral imaging technology, to its users. The partnership, in addition to Nikon's confocal spectral imaging products, brings an affordable and fast spectral imaging solution to widefield microscopy utilizing Nikon's Eclipse 90i and Ti series of microscopes.

 

Paired with Nikon's NIS-Elements software platform, the HSi-300 effectively addresses removal of auto-fluorescence, distinguishes and separates probes with similar emission characteristics, and can be used for brightfield hyperspectral detection techniques in histology and pathology clinical specimens. The new combined platform will also permit easier, more accurate morphological and molecular component differentiation for biological research. Techniques utilizing fluorescence in-situ hybridization (FISH) and preparations using quantum dots (Q-dots) can be rapidly separated and quantified without the use of motorized emission-side filter wheels."

 

For more information go to: MarketWatch.