Digital Pathology Blog

What is your disaster recovery plan?

I was recently asked a question about digital pathology I had never given much thought to.

The question came out of a discussion relating to storage needs for digital pathology, particularly in a full adoption mode for 100% sign-out.  There are matters of capacity, live versus archival, storage time, redundancy, backups, etc...

A colleague of mine recently had his external 1 TB hard drive "crash".  Every powerpoint lecture, reams of research data, manuscripts, personal files & 25,000 mp3 files were thought to be lost.  He neglected to backup any of it obviously.  A commercial service restored the disk with everything but the music files.  We all know this happens routinely.  He did this only recently due to some constraints on enterprise servers and personal storage available on the institutional network and issues with file loss on shared folders with larger capacity.

A clock starts ticking the day you first use such a device that overtime will determine when some mechanical or software function will fail and loss is inevitable, in my opinion.  It has happened to me twice, both after about 3 years of use with varying sized drives and manufacturers.  Both times mirror drives caused no loss of any data.

In pathology we are careful to track what and how much tissue was collected, how may blocks are made, slides from those blocks, stains, recuts, slides sent-out, etc...

As we discuss storage needs and requirements for digital pathology we will have to think about similar issues and disaster recovery plans.

It made me think - what is our disaster recovery plan for stored tissue, wax blocks & glass slides?

I can't recall ever seeing a procedure or policy to address this issue at any institution. 

In case of fire, flood or hurricane what do you do?  What is your lab/institution's policy?

This hospital can trace its roots back to a tornado devastating the town.  The images can always be re-created assuming the real raw data is there to be had.

Digital Microscopy for under 100 bucks? Check out the zPix™ - MM-740

Became aware of this through a pathology listserv as a low cost digital camera (under $100).

"The zPix™ 200 from Carson Optical is a powerful Zoom Digital Microscope that displays the Magnified image right on your computer screen. The impressive 26x-130x Zoom Magnification allows you to see details of ordinary objects you never knew existed! Capture an image to keep using the built-in 1.3 megapixel resolution Digital Camera. You can even capture close-focus video! The MM-740 Zoom Digital Microscope is compatible with the following: Mac OSX 10.4 or later, Windows 98 SE, Windows 2000, Windows ME, Windows XP, Windows Vista. A USB 2.0 port is required.

Also available with a 640 x 480 resolution Digital Camera- zPix™

View some images we took with the zPix"

Raman Molecular Imaging For Digital Pathology

The use of digital pathology techniques without stains or reagents is gaining traction for use in clinical practice, particularly for "gray" diagnostic areas where tride-and-true physical stains and or chemicals may not provide high enough specificity for diagnosis.  I have been following the work being done by ChemImage and their clinical projects with some exciting results.  Check out their offerings and results with Raman and hyperspectral imaging.

Accurate interpretation of pathology specimens can be very challenging for a number of tissue and disease types. Traditional pathological evaluation of tissues and cells is a relatively subjective evaluation of spatially complex stained tissue samples. Since a physician makes treatment decisions based on the evaluation of tissue by a pathologist, accuracy is of the utmost importance.

ChemImage’s Raman Molecular Imaging (RMI) approach using the FALCON II™ enables the objective assessment of tissues without the use of stains or reagents.

              

H&E Stained Prostate Tissue         Raman Image of Unstained Prostate Tissue

(Performed in collaboration with the Mayo Clinic and Allegheny General Hospital)

Raman Molecular Imaging Gives Pathologists:

• Molecular specificity
• Sensitivity to subtle molecular differences
• Measurement of Raman signals from the molecular constituents of a sample without reagents
• Measurements that are spatially localized within a given sample

Raman molecular images are acquired from tissue samples illuminated by a laser in a microscope. The images are analyzed using chemometric-based classification algorithms to objectively classify the sample in terms of disease state. RMI is used to create, in effect, a digital stain of tissues and cells—without the use of reagents.

Related Information

FALCON II™ Wide-Field Raman Chemical Imaging System:
The FALCON II employs high throughput Multi-Conjugate Filters (MCF) and electron-multiplied Charge-Coupled Device (CCD) cameras for Wide-field Hyperspectral Imaging.
Learn More

Application Overview:
Anatomic Pathology Application Overview (PDF 835 KB)

Anatomic Pathology Posters:
Raman Molecular Imaging: A Tool For Investigating Biological Systems (PDF 318 KB)

Hyperspectral Fluorescence Bioimaging (PDF 1 MB)

Diagnostic Utility of Raman Molecular Imaging (RMI) in Separating Renal Oncocytoma from Chromophobe Renal Cell Carcinoma (PDF 697 KB)

Raman Spectroscopy To Predict Prostate Cancer Death After Radical Retropubic Prostatectomy (PDF 359 KB)

Leading-edge Laser Microdissection Technology

With thanks to Dr. Karl Robstad, a pathology resident in Albany, New York for the tip on this offering from Leica.

The new Leica LMD7000 is a laser microdissection system with a power-adjustable, high precision laser. For the first time, high laser power and high repetition rates, are combined within one system.

The laser’s high pulse repetition rates are ideal for the fast excision of single cells, cell clusters, or thin and soft samples. Additionally, high laser power allows the dissection of thick or hard specimens.

Both new Leica LMD6500 and LMD7000 laser microdissection systems use gravity to gently collect the samples. The dissected material, whatever its size or shape, is collected in a contact-free, contamination-free manner. No additional procedures are necessary for collection.

The laser beam movement of the Leica LMD7000 and LMD6500 is controlled by high precision optics, whereas the microscope stage and the sample are both fixed. This allows precise cutting accuracy at high magnifications, as well as high cutting speed at low magnifications. Both are prerequisites to obtain homogeneous material for downstream analysis and reliable results.

Leica Microsystems’ new intuitive user interface eases everyday research. Additional consumables, such as a non-fluorescent, glass-like membrane for all contrast methods, complete the extensive consumables program.

The new Leica LMD7000 and Leica LMD6500 laser microdissection systems are the ideal instruments to dissect live cells, single cells, and specific cell clusters for biomarker research, molecular pathology, and many more applications.

IBM gets nano-view with new super microscope

This sounds like technology that is far superior to current electron microscopy for resolution and depending on cost of course may one day replace the light microscope itself for routine microscopy with nano technologies they claim are "100 million times the display resolution of MRI machines..."

These technologies may also facilitate the convergence of pathology/laboratory medicine and radiology that has become popular in the pathology community with arguments for and against doing so.

January 12, 2009 (Computerworld) -- Scientists at IBM have built a microscope that they say has 100 million times the display resolution of MRI machines used in hospitals.

The new microscope is designed to study complex 3-D structures at the atomic level. Scientists say they're hoping the microscope could help researchers who are investigating diseases and creating new medications.

"This technology stands to revolutionize the way we look at viruses, bacteria, proteins, and other biological elements," said IBM Fellow Mark Dean, vice president of strategy and operations for IBM Research, in a statement.

A year ago, scientists at Lawrence Berkeley National Laboratory announced that scientists had begun using the world's most powerful microscope -- a 12-foot-tall electron microscope that officials said enables researchers to see 3-D images of atomic structures. The Transmission Electron Aberration-Corrected Microscope lets scientists see smaller objects than is possible with a traditional light microscope, according to Peter Denes, director of the TEAM project at the Berkeley, Calif.-based lab.

IBM noted that the resolution of its latest microscope was enabled by a technique called magnetic resonance force microscopy (MRFM), which relies on detecting ultrasmall magnetic forces. The technology boasts high-resolution imaging but also can give scientists a view of the object below the surface. It also reportedly isn't destructive to sensitive biological materials.

IBM said its team, which worked with the Center for Probing the Nanoscale at Stanford University, boosted the sensitivity of MRFM and then combined it with an advanced 3-D image reconstruction technique.

"MRI is well known as a powerful tool for medical imaging, but its capability for microscopy has always been very limited," said Dan Rugar, manager of nanoscale studies at IBM Research, in a statement. "Our hope is that nano MRI will eventually allow us to directly image the internal structure of individual protein molecules and molecular complexes, which is key to understanding biological function."

Last July, researchers at the California Institute of Technology announced that they had developed a high-resolution microscope that is small enough to sit on a computer chip.

The device, dubbed the optofluidic microscope, has the magnifying power of a top-quality optical microscope and is designed so scientists can use it in the field to analyze blood samples for malaria or to check water supplies for pathogens.

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.

 

Caltech unveils ‘microsopic microscope’

The Device Guru has an interesting post on a "microscopic microscope" from Cal Tech. 

Here is the introduction:

Caltech claims its researchers have “turned science fiction into reality” with their development of a single-chip “microscopic microscope.” Although it doesn’t have any lenses, the device is said to provide magnification comparable to that of sophisticated optical microscopes.

The microscope’s magnifying capabilities derive from a technology known as microfluidics, which is based on “the channeling of fluid flow at incredibly small scales,” according to the project. Applications for the so-called “optofluidic microscope” are expected to include field analysis of blood samples for malaria, or checking water supplies for giardia and other pathogens.

OLYMPUS TO LAUNCH FASTER DIGITAL CAMERA FOR MICROSCOPES

07/02/2008 23:38:41

TOKYO, Jul 03, 2008 (AsiaPulse via COMTEX News Network) -- Olympus Corp. (TSE:7733) said Wednesday that it will release this coming Monday a new digital camera that connects to microscopes used at medical sites and for inspections at factories.

The DP72 attaches to the top of the microscope. It has an effective pixel count of 1.45 megapixels and can capture nine frames of images in a single 3 x 3 image array equivalent to 12.8 megapixels. Image capture time has been shortened to 2.5 seconds from three seconds, making work more efficient.

The new camera also has enhanced color reproduction, enabling the display of colors closer to reality. It is expected to help researchers obtain more accurate information in pathology diagnoses.

The DP72 will have a standard price of 1.61 million yen (US$15,212). Olympus is targeting domestic sales of 1,000 units a year.

Olympus OnSite Truck

I had an opportunity yesterday to take a tour and view the Nanozoomer at a recent health fair at my insitution on the Olympus Onsite delivery system.  I might be the last person in this space to see this but it is worth checking out when it comes to a site near you!  A link to a video tour is available here as well as details.  This is a traveling booth on a 18 wheeler that showcases Olympus's microscopes, surgical products and diagnostic systems as well as areas for financial and healthcare services and consumer camera and recorder products.  Olympus is brought directly to you!

Here is a previous press release from Olympus with more specifics.

My personal thanks to the sales and marketing vendor associates for the personalized tour and demonstration.

Megapixel myth

A site created by a photographer, Ken Rockwell at www.kenrockwell.com addresses a variety of issues dealing with digital and film photography, image processing and helpful tips.  Among them are buying guides, technical support and well done photo demonstrations of white balance, sharpening and instrument recommendations. 

Included is a page dealing with the "megapixel myth" which comes up for static and telepathology pathology images when trying to answer the questions "How much resolution is enough?"  "Are the images big enough?"  "What size camera should I buy?" And so forth. 

One issue I come back to frequently is that resolution and little to do with image quality.  Other factors including subject matter, field selection, stain quality, how the image will be viewed, what is/are the questions being asked or what illustrations are provided for are much more important. 

Realize that video telepathology may be sufficient for most cases with a resolution of less than 640x480.  Static telepathology is accomplished with images of that size without compromising the diagnostic features or the quality of the image if the appropriate fields and magnifications are selected.  Robotic systems allow for the same or slightly more with minimal gain in my experience. 

The monitor resolution or DPI obviously is critical.  With that said, I have seen little lost other than desktop space with bulky CRT monitors without flat panel higher resolution screens for diagnostic work. 

This breast cancer image was captured with a 3 MP camera (640x480), originally saved as a TIFF, compressed to a JPEG and further compressed for this posting at a size of less than 300K.  It represents a diagnostic field.  I have used "better" cameras with inferior image quality. 

This time stamped photo of malaria taken from a thin blood film using an oil immersion lens was taken using a 3 MP camera through the ocular of a BH-2 microscope.  You can make out the organisms and speciate accordingly.  Not bad considering the "technology".

Some publishers still insist upon "high resolution" iamges, saved as TIFF for images accompanying manuscripts.  One I recently submitted a paper to required RBG and CMYK formats before deciding if and what would be published in the mode of their choice.  Absurd given the image size, paper and print quality.  It speaks to resolution (linear resolution) in terms of image resolution, print resolution and the issue of screen resolution I touched on above.  There is little difference between 3 and 6 MP.  The difference is nil between 6 and 8 MP.  One needs about a doubling of resolution or film size to make an obvious improvement.  This is the same as quadrupling of megapixels. 

For a print in a journal at column width printed at 300 DPI, the degree of resolution is not as significant as focus, tone, white balance, contrast, sharpness, etc...

The image on the far left was taken with a 6 MP camera, the one on the near left taken minutes later with an 8 MP camera.  Can you tell the difference (other than slight differences during sunrise)? 

The same is true of histology images.  Each of these was taken at 20x with a 2MP camera and compressed so that each one is 1/2 the size of the other from left to right in this pane. 

All are from the same field of a Warthins tumor.  Not only can you make the diagnosis in the most compressed image, there is no difference between the 3 that would or should dissuade one from making the same diagnosis.

I fully realize there are issues with the blog software but the point is the difference is nil regardless.

With that said, I am looking at personal cameras beyond 8 MP now and into double digits (a complete overkill for 5x7 prints, even 8x10 or larger posters).  Part of it is to try to get closer to "film" quality which requires resolution beyond most commercially available cameras. 

For more on this topic, check out Ken Rockwell's discussion on the topic