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I thought I'd note some upcoming Digital Pathology Seminars sponsored by Aperio in Asia and Europe:
For more information on any of these seminars, please click through to a page with more details, and/or contact the Aperio Events Team at events@aperio.com / (760) 539-1193.
SFGate reports Cal, UCSF scientists form cancer research unit:
Scientists at UC Berkeley and UCSF have formed a research center to explore the physical principles that govern the origin and behavior of cancer cells, and how they multiply in humans. With a five-year, $15.6 million grant from the National Cancer Institute, the UC researchers have formed the Physical Sciences-Oncology Center where they will seek to understand the mysterious ways that cancer - its onset and responses to radiation and chemotherapy - are subject to the laws of physics.
The NCI announced the new grant Monday and said that related centers with similar goals have been created at 11 other major universities and research centers, and that all the groups will be collaborating with each other. Physicists, chemists, engineers and mathematicians will be linked with physicians to probe the mechanisms of the disease's many aspects.
Researchers at the Lawrence Berkeley National Laboratory and UCSF's Helen Diller Comprehensive Cancer Center also will be included. The other centers are at Arizona State, Cornell, Johns Hopkins, MIT, Northwestern, Princeton, Southern California and Texas, as well as the Scripps Research Institute in La Jolla (San Diego County), the H. Lee Moffitt Cancer Center in Tampa, and the Memorial-Sloan Kettering Center in New York.
Excellent. A great use of stimulus money, IMNSHO!
I'd like to share a table of all the image file types supported by Aperio software.
When scanning or creating images, you specify a type code. The type code determines the file format and the compression type.
SVS, TIFF, JP2, and JFIF are file formats. (SVS are TIFF files.)
JPEG, JPEG2000, and LZW are compression types.
Some file formats only support one compression type. JP2 files always use JPEG2000 compression, and JFIF files always use JPEG compression. (For this reason, JP2 files are sometimes called “JPEG2000 files”, and JFIF files are often called “JPEG files”.) The SVS/TIFF file format supports multiple compression types, including JPEG, JPEG2000, and LZW, as well as “none” (no compression).
Here’s the full range of type codes supported by Aperio’s software:
(click to download this table as a PDF)
The most common types are type 2, which is JPEG compression in a TIFF/SVS file, and type 3, which is JPEG2000 compression in a TIFF/SVS file.
PS don’t ask what happened to type 6. Just … don’t.
Last Thursday and Friday the U.S. FDA convened an advisory panel of pathologists and statisticians to seek input on regulation of digital pathology. Day one was devoted to scientific and technical issues, and day two was study design and other regulatory considerations.
Each day began with some presentations by invited speakers and FDA scientists and examiners, followed by lunch, and then one hour was set aside for “public” speakers; basically anyone could ask for a speaking slot, and they ended up being six minutes each. Following that, on each day the panel was asked to debate and answer a series of questions posed by the FDA.
I have posted the FDA advisory panel Agenda (which includes a roster of the panel members), the Questions posed by the FDA to the advisory panel, and a Background Briefing document provided by the FDA.
Day One: Scientific and Technical considerations for digital pathology
Lunch! After lunch was an hour set aside for public speakers, of whom there were seven, each given a six minute slot.
After a break the FDA questions for the panel were presented and discussed. (See Questions document, Day One.)
Day Two: Study characteristics and other regulatory considerations for digital pathology
Lunch! After lunch there was an hour set aside for public speakers, there were six.
Next the FDA questions for the panel were presented and discussed. (See attached Questions document, Day Two.)
There was a short break, after which it was noted that further comments could be submitted by *anyone* to Maria Chan (maria.chan@fda.hhs.gov).
And so ended the panel discussion. All in all a fascinating and informative couple of days, and I believe the FDA got a lot of good information they can use for deciding how to regulate digital pathology systems going forward.
I'd like to welcome pathologist Gregory Henderson to the blogosphere; his new blog is called The Primary Care Pathologist. In his first post he describes The Primary Care Pathologist's DNA, and in a follow up post he wonders if You Might Be a Primary Care Pathologist:
In addition to being a Primary Care Pathologist, I think he is a natural born blogger; great stuff. Subscribed!
The NY Times has a nice article today about MD Anderson: A place where Cancer is the Norm.
M. D. Anderson Cancer Center has a mission statement, and everyone who works there, from the president to the cleaning crews, can state it like a catechism: to “eliminate cancer in Texas, the nation and the world.”
For the nearly 90,000 patients who will go to the center in Houston this year, that mission cannot be fulfilled soon enough. They and their families arrive at the world’s largest freestanding cancer hospital from around the world, often leaving behind jobs and stashing children with relatives for months. Some rent apartments or stay in mobile home parks near the hospital.
They enter through a soaring lobby, with cheery aquariums and exuberant volunteer greeters eager to help in any way. They come looking for hope. But there is no mistaking what this place is: the front line of the frustrating war on a still largely incurable disease. Doctors are encouraged to try everything, and when insurers balk, they pick up the phone, repeatedly, hoping to persuade them to pay for what may be unconventional treatments.
Pretty inspiring; how great is it to have institutions like this on the front lines. And great progress has been made, although there is so much left to do. Just shows how difficult the fight against cancer really is...
Wow, CAP Today now has a spiffy online edition. Really cool, especially for those of us traveling on airplanes (as I am at the moment, with WiFi and power, thank you Virgin America).
Excellent, by all means check it out!
The FDA are convening a public advisory committee tomorrow and Friday Oct 22-23 to discuss discuss and make recommendations about "public health issues" related to the use of digital whole slide imaging (WSI) systems. They have posted a briefing document.
The FDA is sponsoring this 2‐day Advisory Panel meeting on Digital Pathology Whole Slide Imaging (WSI) to gather expert information for how to ensure that the current standards of safety and effectiveness of routine surgical pathlogy will not be compromised if digital WSI is used as a substitute for the conventional light microscope. For over 100 years, the reference method for the diagnosis of cancer and many other critical clinical conditions has been by histopathology using he conventional light microscopy. This process and medical practice is known as surgical pathology in the United States.
Digital pathology is the use of computer technology to convert analog microscopic images into digital images that are similar to digital photography. Digital WSIs do not replace the glass microscope slide. The glass microscope has to be prepared just like with the light microscope and is the source of the information to be digitied. However, there are many functions that digital WSIs offer that are not possible with light microscope examinations. These include the integrating the workflow of the pathologist with the electronic medical record, retrieval of previous biopsy images using the computer, split screen comparison of 2 or more images from the same case or different cases, ability to use WSI data for computer‐assisted image analysis and manipulation, transmission of digital images to the patient’s electronic chart, the internet and other links, and so forth.
The panel will hear presentations from a variety of experts and FDA officials, and also a number of individuals who have registered to speak during the public comments portion of the agenda (such as me; I plan to present some remarks about Measuring Accuracy in Digital Pathology).
The FDA have posed a number of questions that they would like the panel to answer; the ultimate result will probably be a guidance document for companies filing for clearance or approval of their devices for various applications in digital pathology. It should be a fascinating and informative couple of days; please stay tuned for a report!
LabSoftNews posts Physicians Using an iPhone Application to Triage Their Patients. This is an article about iTriage, an application which assists physicians in referring their office patients to regional hospital emergency rooms when necessary. Seems like a perfect use of smartphones aka handheld computers.
The question of interest to me is when iPhones and other handheld computers will be useful for viewing digital pathology images. And note I ask when and not if; it does seem only a matter of time. But the small screens, relatively weak processors, and relatively slow network connections of smartphones make them poor candidates for viewing pathology images. Still it might be far better than nothing to a pathologist traveling or away from her desk in case of a consult or frozen section or some other immediate viewing need.
We've had the ability to view digital slides on smartphones via a web interface for nearly two years, but although it makes a nice demo, my sense is that people aren't really using it for actual casework. That could change, and a dedicated application might make sense when it does.
Sorry for the long absence; yes, it has been a month since the last chalk tip. But I have a great one for you today; how to demo conferencing on ONE computer. You will not need a network!
This tip assumes that you have a working Spectrum system; you can log on, list digital slides, and view them with ImageScope. Okay? Here we go…
1) Make sure ImageScope is NOT running. If it is, close it :)
2) On the Windows taskbar, click Start | Run and enter “imagescope /m”. This will start ImageScope. (The “/m” means “multiple” :)
3) Now do it again, click Start | Run and enter “imagescope /m”. Yes, you will have two count ‘em two copies of ImageScope running.
4) This is the tricky part, arrange the windows so you can see both of them at the same time. Put one in the upper right corner, and one in the lower left corner. Something like this:
5) Okay, now we’re going to start a Digital Slide Conference from the upper right ImageScope. Select View | Digital Slide Conferencing from the upper right ImageScope’s menu. Position the Digital Slide Conferencing right next to the upper right window, like this:
6) Now click on the DSC Server… button. You will see this dialog box:
Enter “localhost” into the Server Name field, as shown, and “84” for the Port, and enter a Screen Name so you know which ImageScope is which; for example, “upper right”. Then Click Login.
7) You will see a message that says: Connected: localhost:84:
8) Now click the Create Conference button, enter a conference name (e.g. “my test conference”), and click OK. This creates a conference and logs you into it. The DSC conference window will look like this:
9) COOL! Now we’re going to join the conference from the lower left ImageScope. Select View | Digital Slide Conferencing from the lower left ImageScope’s menu. The DSC window for this ImageScope will open right over the other one; move it next to the lower left ImageScope, like this:
10) Now click on the DSC Server… button. Again you will see this dialog box:
Make sure Server Name is set to “localhost”, and Port to “84”, and enter a Screen Name to identify this ImageScope, such as “lower left”. Then click Login.
11) Almost there! You will see a message that says: Connected: localhost:84:
12) Now click the Join Conference button, and you’ll have a conference with two participants, “upper right” (the current leader) and “lower left”. The DSC windows for the two ImageScopes will look like this:
13) That’s it! You’ve established a conference between two ImageScopes running on ONE computer. Yay.
Now you can demo conferencing… using Spectrum, open an image; it will be opened in the upper right ImageScope, and then in the lower left ImageScope also. Pan and zoom in the upper right ImageScope, and the image will be panned and zooming in the lower left ImageScope. Use the Assign buttons to switch leadership of the conference, or use the Request checkboxes and Relinquish buttons. Check the “Show Mouse” checkbox to enable the red “laser pointer”. You can open more than one image at once. Etc. Have a great time :)
I hope this helps; conferencing is a cool feature, and now when you have only one computer you can still show it off! Try this on your next airplane flight, and you’ll be good to go…
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