The Daily Scan

Longitudinal Brain Scan Study Shows How Brain Matures

From FuturePundit, Longitudinal Brain Scan Study Shows How Brain Matures:

The brain's center of reasoning and problem solving is among the last to mature, a new study graphically reveals. The decade-long magnetic resonance imaging (MRI) study of normal brain development, from ages 4 to 21, by researchers at NIH's National Institute of Mental Health (NIMH) and University of California Los Angeles (UCLA) shows that such "higher-order" brain centers, such as the prefrontal cortex, don't fully develop until young adulthood.

A time-lapse 3-D movie that compresses 15 years of human brain maturation, ages 5 to 20, into seconds shows gray matter - the working tissue of the brain's cortex - diminishing in a back-to-front wave, likely reflecting the pruning of unused neuronal connections during the teen years. Cortex areas can be seen maturing at ages in which relevant cognitive and functional developmental milestones occur. The sequence of maturation also roughly parallels the evolution of the mammalian brain, suggest Drs. Nitin Gogtay, Judith Rapoport, NIMH, and Paul Thompson, Arthur Toga, UCLA, and colleagues, whose study is published online during the week of May 17, 2004 in The Proceedings of the National Academy of Sciences.

This is just amazing, please see the article for more information and a lot of links to other resources about brain development.

Win an Apple bioinformatics system

Apple is sponsoring a competition for bioinformatics projects, and they're giving away five bioinformatics workgroup clusters as awards! This is really cool.

I'm going to apply on behalf of Aperio; these systems would be perfect for running our pattern recognition algorithms against large virtual slides.

Aperio WebViewer documentation update

The Aperio WebViewer documentation has been updated to reflect support for SIS files and linking ImageScope from web pages.

This document describes the installation and configuration of the WebViewer, as well as how to link to Virtual Slides (including specific regions of slides) and how to integrate the WebViewer into second- or third-party web pages.

It's all "open" information - please download the document and let me know if you have questions or comments.

The Killer

I've been posting recently about Cancer, and how various forms of cancer are now the leading cause of death in the U.S.  This interest is personal - I've lost my father to cancer, as well as some close friends - and professional - Aperio's customers are the Pathologists who diagnose cancer and researchers attempting to cure it.  Recently I came across some comprehensive statistics from the American Cancer Society which quantify the problem.  A summary of these statistics is shown at right.

In the U.S, in 2004, over 560,000 people will die as a result of cancer.  That's about the same as the entire populations of Boston or San Francisco.  Wow, talk about a killer.

This sure puts the U.S. combat deaths in Iraq in perspective.  As of May 11, 560 U.S. servicemen have been killed in Iraq, three orders of magnitude fewer than will have been killed by cancer this year.  I don't want to minimize those deaths - at all - merely to put them in perspective.

At least we can get up in the morning knowing we're working on the right problem.

TMA Report

Select Biosciences has a new report on Tissue Microarrays. The report costs $2,995, but the abstract contains some interesting statistics:

The market for tissue microarrays is set to grow at 42% per year from $ 13 million in 2002 to over $163 million by 2008.

State of the Market, 2004

• TMAs as product - competition is high
  Many acedemic institutions and pharmaceutical companies obtain tissue microarrays for their use either in-house or in collaboration with other institutions.
• TMAs as service - competition is low
  As the use of TMAs for different applications increases, the demand for services will go up. Increased demand of customized services will also grow with the increased use of this technology in clinical trials.

(click to view TMA slide)

TMAs are difficult and time-consuming to scan with conventional tiling methods; the Aperio Scanscope is an ideal device for scanning TMA slides. Aperio also has a software application named TMALab which automates cell segmentation and simplifies analysis and data entry for TMAs.

Linking to Virtual Slides

We've added a new feature to Aperio's web viewing technology. You can now link to Virtual Slides on web pages for viewing with ImageScope.

Aperio has two ways to view Virtual Slides - you can use our WebViewer, which is flash-based and integrates into web pages, or use ImageScope, which is a Windows desktop program. Each way has advantages. The WebViewer is cross-platform, and users can view slides without any downloads or installations. ImageScope is faster and has many features which WebViewer does not have, including annotation authoring, the ability to view multiple slides at once, image color/gamma adjustment, etc., but it does require that users download and install software.

When you visit a gallery of slides online, such as Aperio's slide gallery or the galleries at scanscope.com, you will notice a new feature. Each image is now displayed with a dark green link labeled “(open with ImageScope)”. Clicking these links causes ImageScope to be launched on your desktop to view the associated slide. You need to have ImageScope installed (v4.14 or later) for this to work. (You can download the latest ImageScope from our website - it's free.)

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In case you’re wondering how this works, here’s the magic. ImageScope now supports a new kind of file – a SIS file – which is a text file that lists one or more images to be opened. This file functions like a pointer. If you open ImageScope with a SIS file it simply opens each of the files listed in the file. (SIS stands for “ScanScope Image Set”.)

There are [at least] two use cases for SIS files. The first is this one – it makes it easy to create web links for ImageScope. To link to a Virtual Slide, you create a SIS file that contains the Virtual Slide’s path and link that on your website. When someone clicks the link it causes the SIS file to be downloaded, Windows opens the application associated with the file (ImageScope), and then ImageScope opens the image. This works nicely because SIS files are so small.

Some customers have linked directly to Virtual Slides – the SVS or JP2 files. This causes the entire file to be downloaded into a local directory, and then ImageScope is launched. It will work on a local network – not that well! – however it won’t work on a wide-area network at all.

The same "indirect file" technique is used by Windows MediaPlayer and RealPlayer to point to streaming movies.

The other use case for SIS files is when there are multiple images associated with a case. Each case can have a single SIS file associated with it that lists all the virtual slides for the case. Opening the SIS file then causes ImageScope to open all the virtual slides for the case at once.

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Even more technical detail: SIS files are really just little XML files. They have the following format:

   <SIS version=”1.0”>
      <Image>
         &ltURL>path</URL>
      </Image>
   </SIS>

There can be multiple &ltImage> tags in a file, in which case multiple images are specified. Each image's <URL> may be specified as one of the following:

C:/directory_path/file.ext
	- Windows file (only useful locally)
\\server\directory_path\file.ext
	- path to file on Windows network share (backward slashes)
//domain/directory_path/file.ext
	- path to file on remote ImageScore server (forward slashes)

The last format is the one typically used on a website.

One final note – it isn’t always necessary to actually create the SIS files, the SIS data can also be generated programmatically. For example, the WebViewer generates the SIS data dynamically. It wasn’t necessary to create a SIS file for each file hosted on scanscope.com.

DNA bot targets cancer

This is pretty amazing; AlwaysOn reports DNA bot targets cancer.

Researchers from the Weizmann Institute in Israel have constructed a molecular-size computer that is programmed to find signs of cancer cells, and when they are present, dispense DNA molecules designed to eradicate those cells.

The computer is small enough that one trillion of them fit in a drop of water and consists of three modules made from strands of DNA: input, computation and output.

The input module strands contain stretches of bases that pair up with and so identify certain stretches of messenger RNA. The computation module processes a series of input modules to determine whether the balance of certain types of messenger RNA indicates the presence of cancer cells. The output module administers a drug in the form of another DNA strand when cancer cells are indicated.

The present is looking more like the future every day.

DNA Ultra-Conserved Sequences

FuturePundit notes DNA Ultra-Conserved Sequences Found Between Humans, Mice Rats:

Hundreds of stretches of DNA may be so critical to life's machinery that they have been “ultra-conserved” throughout hundreds of millions of years of evolution. Researchers have found precisely the same sequences in the genomes of humans, rats, and mice; sequences that are 95 to 99 percent identical to these can be found in the chicken and dog genomes, as well.

Reusable code is important in software, I guess it is the key to life :)

Human Brain to Machine Interface May Now Be Feasible

Medscape reports Human Brain to Machine Interface May Now Be Feasible:

Directly using human brain neuronal activity to operate external neuroprostheses may now be feasible, according to a presentation on May 4 at the 72nd annual meeting of the American Association of Neurological Surgeons held in Orlando, Florida. This work could potentially benefit patients with quadriplegia or other focal neurological injury who are unable to use their extremities because of a breakdown in connectivity between their limbs and brain motor centers.

Wow.

Apropos, I just started reading Broken Angels, from Richard K. Morgan, a sci-fi thriller which is a sequel to his wonderful Altered Carbon. In his 25th century world people can have "neurochem" enhancers and prothesis which are brain-activated. It might really happen, and sooner than he imagined!

Rendering Images in 3-D

The Scientist has an interesting article about Rendering Images in 3-D:

To the uninitiated, three-dimensional microscopy makes the pretty pictures of fluorescently labeled cells that grace the covers of scientific journals. But to today's microscopists, the capacity to render images from 3-D and 4-D datasets is critical for studying the distances between objects in a sample and for tracking how complex samples change over time.

The article discusses many of the techniques commonly used for 3-D imaging, including confocal microscopy and deconvolution (illustrated in picture at right).

Aperio's ScanScope digital slide scanner is capable of scanning microscope slides at multiple Z-levels, yielding a 3D dataset. This is particularly useful for cytology preparations and other "thick" specimens. Please click here for an example of 3-D virtual slide viewing.