Crowd Sourcing and Anonymous Science

Maybe the future of science will be in the form of crowd-sourced anonymous discussions, which will be used to formulate testable hypotheses and experimental design.  Then publicly funded labs would pick up the work, perform the experiments, and publish the results.  The results would then be discussed by the anonymous crowds.

The anonymity is crucial, because it would act as an objectivity filter.  The mechanism of anonymity would specifically act to prevent the formation of visible "personas", because comments would not be traceable to a known identity.  So over time the discussions would assume the form of a "collective mind" debating with itself.

WarpTPS

One of the problems to be addressed for adaptive treatment paradigms is the need to visualize and interact with deformable vector fields (DVFs).  While a number of techniques exist for visualizing vector fields, such as heat maps and hedgehog plots, a simple technique is to allow interactive morphing to examine how the vector field is altering the target image to match the source.

WarpTPS Prototype

This is a very old MFC program that allows loading two different PNG images, and then provides a slider to morph back and forth between them.

Note that currently the two images that can be loaded through File > Open Images... must have the same width/height, and are both required to be in .BMP format.

First is a video of Grumpy to Hedgy:

And this, slightly more clinically relevent example, shows one MR slice being morphed on to another one:

pheonixrt has a new home!

I just recently completed the GitHub migration, due to Google Code shutting down.

https://github.com/dg1an3/pheonixrt

Three projects are represented:

• pheonixrt is the original inverse planning algorithm based on the convolutional input layer
• WarpTPS is the interactive morphing using TPSs
• ALGT is the predicate verification tools

Also, see the references at the end of http://en.wikipedia.org/wiki/Thin_plate_spline for some videos showing WarpTPS.

d3

I've been starting to look at d3, and what kinds of cool things can be done with it.  The examples are pretty nifty, especially as a starting point for more complex things.

To get a feel for the code under src\, I made a code tree map:





Basically I followed the same formula; on a local PC I placed the d3 javascript and then ran:

for /S %n in (*.js) find /C ";" %n >> output.txt

which produces a list of line counts with at least one semicolon.  Then I imported the result in to a Google spreadsheet, sorted and removed unnecessary files, and then created the treemap.

ClearCanvas and RT Objects

I'm looking at the source code for ClearCanvas and wondering aloud how hard it would be to modify to store RT objects.  For instance:

• Current generation DICOM RT SOPs
• Supplement 74 objects
• Patient positioning objects
• Next generation DICOM RT SOPs

Of course, rendering the objects in the Volume.MPR viewer would be especially cool, but one step at a time...maybe registering a replacement for ImageReview3DForm would be a logical next step.

The Open Source Patent

Does patent rhyme with open source? Think about it this way - the original GNU Public License is a form of managing intellectual property based on copyright protection. A restriction _is_ being placed on the intellectual property licensed with GPL, specifically that modifications cannot be held proprietary. If open source did not place any restrictions on intellectual property, then Public Domain would have been sufficient and there would be no need for the GNU Public License. That the restriction is a permissive one (aimed at increasing the availability of the source code) does not affect the fact that open source licensing requires being able to legally restrict the kinds of things that can be done with the intellectual property.

So, is copyright a sufficient mechanism to propagate open source? If a closed-source company encounters a particular piece of code that it likes, why couldn't it simply take the code, make some nominal change so as to avoid copyright infringement, and then incorporate it in to its proprietary products? This has probably happened on a number of occasions already.

If the source code embodies a truly novel or innovative feature, then the copyright basis of current open source licenses may be too weak. In this case, adding a patent (provided the feature is patentable) as an adjunct to the open source license can help to minimize the temptation of closed source companies to simply reverse engineer the feature and incorporate it in to their product. Of course, it should be agreed that the patent should not be used to restrict the open source propagation of the intellectual property (which is specified in more recent versions of the GPL, I think).

Innovation and Risk

Having recently completed the first phase of a new inverse planning algorithm for radiation treatment planning, I have been thinking a lot about the relationship between innovation and risk. Of course, everyone knows that innovation is intrinsically risky, but the question is: what are all of the components of this risk, and can all be mitigated as efficiently as possible?

The commitment of time and resources to the initial development of a new idea is one of the first sources of risk in innovation. This risk can best be managed by following a path that develops the innovation to a suitable state for evaluation, while expending a minimal amount of resources.

But once this point has been reached, there is still further risk that persists, due to the need to couple further development to pragmatic concerns of how the innovation is to be used (productization). While this will consume even more resources, it seems that the current market(s) for innovation could benefit from significant improvements in efficiency of how this risk is mitigated.

For any new innovation, there will always be some early adopters who would be willing to expend some of their own resources toward the productization of a promising new technology. The problem is that this early adopter's risk is not efficiently mitigated, because the adopters themselves seem to only get intangible benefits from this risk. For instance, a high-profile clinic with many researchers will undertake new technologies because it allows their researchers to maintain their status as cutting-edge innovators. This means that, when deciding which innovations to adopt, they will mostly evaluate the likely "halo effect" of being associated with a ground-breaking new technology, which is an intangible benefit that eludes quantitative evaluation. Thus they will tend to be looking for "blockbuster" technology, much like Hollywood makes money mostly on a few blockbuster movies. Smaller independent films need financiers who are more willing to undertake smaller risks for smaller possible benefits, in return for equity interest.

But why can't early adopters in technology also partake in "equity interest" of some sort for their risk? This might encourage more commitment of resources during the productization phase of innovation, which would then make the initial development phase correspondingly less risky as well.