Moving!

•25 April, 2012 • Leave a Comment

Sorry for the lack of updates — I’ve been really busy with school, and moving the website so it suits my needs a bit more (becoming more of a portfolio-with-a-blog rather than just a blog).

But now the new website is done! It’s now at http://www.asymptoticdesign.org/, and I’ll be updating stuff there for now on — so be sure to check there often:)

All of the current blog material has been moved over to the new site, and will remain here for the foreseeable future.

OpenScope Software v1.0

•29 March, 2012 • 1 Comment

School has a way of keeping you busy. Very busy. But don’t worry; I’ve been working hard at building awesome stuff! In particular, I’m still making progress on my open microscope design. The fluorescence works, but I’m still in the stages of trying to optimize it (and seeing if I can reduce the cost of the final design). However, I’ll probably make another post soon with some proof of concept images and a general outline of how it works. While the physical microscope is still in the works, I managed to make some serious progress in writing software for it!

I’ve always been surprised at how expensive professional microscope imaging software is, and how *repetitive* the tasks are for it. It’s almost like photoshop… you just need a ‘count number of particles’ button, a ‘calculate intensity’ button, ‘calculate area’, and so on… So I figured I’d try my hand at writing some basic image analysis software and see where it takes me.

The result is ‘OpenScope Software’, which I intend to release as a software package to go with the hardware for OpenScope. Right now there’s two tasks I want to be able to do with fluorescence microscopy:
-Calculate the intensity/brightness of a selected region of interest
-Track that region of interest across a sequence of images so I can track the fluorescence vs. another parameter (such as optical sectioning, introduction of a drug, etc.).

OpenScope software uses Python Imaging Library and TKinter to do just that. It creates a RegionOfInterest object that track a region of interest, can draw a box around it, and computes values using the pixel data (including when the pixel data changes). It also has a Sequence object that handles loading a series of images labelled numerically (such as image01.jpg, image02.jpg, image03.jpg… until the last image) so that you can perform image analysis on optical sections or videos of fluorescence microscopy.

Example of OpenScope Software v1.0

The code is available on github here: https://github.com/asymptoticdesign/openscope-software; the README file includes the instuctions for the few features it has, along with a test image.

Coming Soon: Some more software features and a physical fluorescence microscope to go with it!

Doodles in Processing

•16 March, 2012 • Leave a Comment

I’m teaching a class on Processing at CEMMI (the Collaborative Electronic Mixed Media Institute) this month, which has led to me doodling in processing much more than usual!

The class I’m teaching is focused on teaching how to make generative and visual art in Processing; the class starts with basic concepts in programming (like control flow) and Processing (like colors and primitive shapes), gradually adding concepts like randomness and complexity to really make Processing shine. The current notes (and lots of programming exercises!) for my class are available in their own github repo. I’ll be adding materials there for the next two weeks until the class is over; by then the entire course should be available online!

And now its time to show some neat processing sketches I’ve been working on! This first one was inspired by the work of Rachel Boyce, who did a really neat sketch utilizing overlapping spirals. I was so impressed with her work that I decided to modify it myself! I called this piece ‘Moire Spiral’ because the overlapping lines give yet another moire-type pattern (you can tell that I am an enormous fan of these patterns!).

Moire Spiral on openprocessing.org

The next piece is called ‘Search Light’, because it is reminiscent of a searchlight searching for something in the night. It was actually generated from code that was meant to make a ball travel in a circle; I next made the ball move in a circle modulated by Perlin noise, and then finally drew a line from the origin (top-left corner) to the ball. If you look closely at the tip of the ‘searchlight’ you’ll notice that its still moving in approximately a circle!
Search Light on openprocessing.org

This last one was a further modification of ‘Search Light’; instead of having one point fixed at the origin, I had both points of the lines moving in overlapping circled overlapped by noise. I really like the aesthetic effect here — it almost looks as if there is a long ribbon turning and rippling through space. Check it out!
Search Ribbons on openprocessing.org

I’m hoping to write more about my microscope this weekend; it’s coming along quite well and now it’s a full-fledged fluorescence microscope! Hopefully I’ll get some sweet pictures of the images it can turn out in addition to some more schematics.

DIY Scope

•10 March, 2012 • 5 Comments

For MIT 6.123/20.345 (Bioinstrumentation) I’m building a bright field/fluorescence microscope from scratch; it’s surprisingly cheap (for a serious microscope) so I thought I’d share what I’ve got done.

Conceptually, a bright field microscope needs surprisingly few specialized parts (a bright field microscope is what most people think of when they think of a microscope — you see an object backlit by the microscope light). Most of the magic happens in the objective — and those are readily available from the optics supplies like Thorlabs or Edmund Optics. Besides the objective, you’ll need a couple of convex planar lenses (not too difficult to come by) to focus the beam, and a mirror to help with alignment.

A simplified schematic of the optical path is below:

DIY Bright Field Microscope Schematic

A red LED is used to provide the brightfield light; technically a blue LED would be better (because blue is a smaller wavelength and therefore provides a higher resolution), but would make things a bit messy when I integrate fluorescence later on. The LED light hits the sample and scatters from it; the objective collects the light and needs a 200 mm lens (f1) to correctly collimate the light. The collimated light gets directed to the middle of the camera’s field of view with the mirror, and voila, you have a microscope!

Here’s an image of my constructed microscope (made from mostly Thorlabs’ parts):

DIY Microscope

I tested it using a standard with line thicknesses of known size:

Picture of the standard

and could detect the smallest lines (~18 lines/mm) with pretty good resolution:

Image of the standard through my microscope

I also used a target with 600 lines per mm (meaning the lines should be around 1.6 um apart), and was able to resolve the lines. So we’ve got a resolution of around a single micron on this microscope — enough to make microspheres and most cells visible as blobs.

A 600 line per mm standard, as seen from the brightfield microscope

Right now I’m working on adding a green laser to the optical path for fluorescence microscopy, and figuring out a way to reduce the cost of the microscope. It looks like the final fluorescence microscope will cost in the $1000-$2000 range (in large part because of the camera); I’d like to drop that cost down by about $1000 ideally to the $500-$1000 range. If anyone knows of a good place to get cheap (but not crappy) optics, computer vision cameras, etc., let me know!

Responses to the Federal Research Public Access Act

•6 March, 2012 • Leave a Comment

I woke up today planning to mail out letters of support to my representatives about the Federal Research Public Access Act. While printing out the letters in my office, I found out that the Alliance of American Publishers (on behalf of over 80 scholarly publishers) sent out letters stating their opposition to the FRPAA. Of course, these publishers include giants such as Springer, Elsevier, John Wiley & Sons, and Cambridge University Press.

Let me review their primary arguments:

It requires that final manuscripts of researchers’ journal articles that explain, interpret and extensively report the results of federally-funded research — manuscripts which have undergone publishers’ validation, digital enhancement, production, interoperability and distribution processes — be publicly available online, worldwide, no more than six months after publication.

Let’s view the text of the bill, shall we?

SEC. 4. FEDERAL RESEARCH PUBLIC ACCESS POLICY.
(b) Content- Each Federal research public access policy shall provide for–
(1) submission to the Federal agency of an electronic version of the author’s final manuscript of original research papers that have been accepted for publication in peer-reviewed journals and result from research supported, in whole or in part, from funding by the Federal Government;
(2) the incorporation of all changes resulting from the peer review publication process in the manuscript described under paragraph (1);
(3) the replacement of the final manuscript with the final published version if–
(A) the publisher consents to the replacement;
and
(B) the goals of the Federal agency for functionality and interoperability are retained;

Seems to me that this bill wants the final peer-reviewed paper submitted to the journal, but does not require the final published manuscript with the publisher’s “validation, digital enhancement, production, interoperability, and distribution process” (does anyone else want to know what the heck those words even /mean/?). The alliance’s next point:

The one-size-fits-all six-month deadline for every federal agency that funds research ignores well-known significant differences in how each research discipline discovers and uses individual articles, periods that can last several years before costs are recovered.

First off, the bill is not one-size-fits-all. To visit the text again:

SEC. 4. FEDERAL RESEARCH PUBLIC ACCESS POLICY.
(6) long-term preservation of, and free public access to, published research findings–
(A) in a stable digital repository maintained by the Federal agency; or
(B) if consistent with the purposes of the Federal agency, in any repository meeting conditions determined favorable by the Federal agency, including free public access, interoperability, and long-term preservation.

So each federal agency is allowed to come up with their own repository, as long as they are making a good-faith effort to follow the spirit of the bill. Back to the AAP’s letter:

It limits where government-funded researchers may publish their work.

I can’t find any text in the bill to counter this with because the bill simply does not say this. The only thing that could possibly limit where an author could publish their paper is the publisher’s copyright policy. This act does absolutely nothing to change that. Let’s see what the AAP has to say next:

It undermines publishers’ investments in new business models that currently provide unprecedented access for the public to such works for free or at modest cost.

You couldn’t possibly be referring to Springer’s Open Choice publishing policy, that offers open access for the modest cost of $3000.00 for the author, could you? Or perhaps you mean Elsevier’s Open Access Policy, which charges authors $3000 a pop? How generous of you! And the AAP’s final point:

At a time when Congress is looking to cut unnecessary expenses in federal government and focus budgets on priorities, FRPAA imposes additional costs on all federal agencies by requiring them to divert critical research funding to the creation and management of new databases, archives and infrastructure to handle dissemination of these articles — functions already being performed by private-sector publishers.

Are you serious? The (direct) maintenance cost of arXiv is a tad under $600,000 a year. According to the NSF’s Funding Profile, they awarded 8,509 grants with an average grant size of $165,000. That means that an open access archive would cost as much about about 5 research grants. If multiple federal agencies shared a single archive, the cost could be amortized to less than one grant a year.

As an additional note: the FRPAA only applies to federal agencies with extramural research expenditures (meaning: they give out grants summing to more than) $100,000,000. One hundred million dollars. That means that the arXiv would cost an agency about 0.6% of its external research budget. What do you think their internal budget looks like? I bet it’s a drop in the bucket.

After reading through the above letter, I finally mailed out letters to all three of my representatives — Senators Scott Brown and John Kerry, and Congressman Michael Capuano — asking them to co-sponsor and/or otherwise support the Federal Research Public Access Act. The contents of my letter is below:

Dear [Representative]:

I am writing to ask you to co-sponsor the Federal Research Public Access Act of 2012 ([S.2096/H.R.4004). This bill provides an important mechanism for ensuring that American taxpayers have free open access of peer-reviewed scientific articles funded by U.S. government agencies. It continues a growing trend by both federal agencies and higher education institutions to prioritize open access of research results

One of the fundamental goals of science is not only to perform research, but to disseminate the results to the rest of the scientific community. Yet the cost of journal subscriptions and witholding of research results prevents knowledge from being disseminated as widely as possible; this stunts the rate of scientific discovery by forcing scientists to constantly recreate each others’ work. As the old saying goes, “Six months in lab can save you an afternoon in the library” – without access to current research, countless hours of research efforts are going to waste.

As both a student and researcher at the Massachusetts Institute of Technology, I have access to all of the scientific journals that my institution subscribes to. I use them nearly every day in my professional life; however, I also have access to these manuscripts for projects unrelated to my professional duties. Significant work that has helped others has come out of my efforts as an entreupeneur and citizen-scientist – and much of it would not have been possible without access to up-to-date scientific research. As both a potential author and subscriber to research affected by this bill, I enthusiastically support it.

Not only does the FRPAA provide open access, but it is flexible with regards to the interests of journal publishers and federal agencies. The bill asks agencies to develop their own individual general guidelines, recognizing that there is no ‘one-size-fits-all’ solution. The bill provides an exclusive six month window for journals to provide access to the published material, and only peer-reviewed manuscripts (not the final published edition) are required to be made available.

Please support and consider co-sponsoring the Federal Research Public Access Act of 2012.

Thank you for your time,

Nathan S. Lachenmyer

My position as a researcher (at MIT, no less) puts me in the minority of people that have access to most peer-reviewed publications out there. I’ve used that wealth of knowledge to learn more about current research, help me find solutions to difficult problems in classes and personal projects, and even in my recent work at H@cking Medicine (where I used sensors to come up with a quantitative way to measure symptoms of patients diagnosed with Parkinson’s Disease). A large portion of this work would have never happened without access to current publications; and for that reason alone I want to enable others to have that same experience.

I encourage you to send a letter to your representatives! Here’s how:
-Find out who your representatives are via services at the websites of the House and Senate.
-Write a letter to your representatives! Feel free to use reuse parts of my letter above. The Alliance for Taxpayer Access has some great talking points as well.
-If you’re feeling like being extra active, please support the sponsors for the bills — a list of the sponsors in the Senate and House are readily available.

Open Access Research

•4 March, 2012 • 1 Comment

As someone that is an avid advocate of open source software/hardware (both for my creative endeavors, as you’ve seen here, and my scientific endeavors as a researcher at MIT) and a member of many DIY/Maker/Hackerspace communities, I try to keep tabs on the status of open science/open access. The idea is simple — one should not need a pedigree (or, in this case, a degree) to participate in science! Scientific information, techniques, data, and results should be made available to anyone that desires access to it — and should be replicated by anyone who can capably (and safely!) reproduce the author’s efforts.

In the last month or so, the issue of Open Access Research has really taken center stage in the scientific community. A boycott against Elsevier (one of the three largest scientific publishers) was initiated, which snowballed into increased awareness of the Research Works Act. This wild month of attention came to a surprising turning point this week: Elsevier officially withdrew its support for the RWA, effectively killing the bill.

For those of you who aren’t aware of the significance of what I’m talking about, let me provide some background information:

The Problem

Traditionally, research journals have existed to assist in the dissemination of (scientific) information. Academic journals have existed since the mid-1600s, where the job of accumulating work by scientists, typesetting it, printing the journals, and distributing them was a non-trivial task that required a great deal of man-hours and resources. During the early days of journals, they served an invaluable role is the process of disseminating scientific knowledge to researchers around the world.

Typically the editorial board of such a journal consists of distinguished scientists (usually university professors) from a specific field (e.g. a nuclear physics) that manage the process of selecting articles for publishing. These editorial board members are usually volunteers; their role on the board of a journal is considered to be both an honor and a part of their scholarly duties. The editorial board typically matches submissions with referees, whose job is to evaluate the paper’s scientific merit (these referees are also volunteers, and often university professors/researchers). If the referee and editorial board decide to publish a submitted paper, the author (also typically a university professor or graduate student) is then required to sign over the copyright for their work to publisher, and receives no financial compensation for their work — after all, they chose to be scientists to do research that will further humanity’s body of knowledge and hopefully improve our lives. Sharing of results is an integral part of research.

So where do these papers go? Well, many of those some researchers who participated in submission process. They are either directly subscribing to these journals, or more frequently, their university has a subscription to these journals.

Before the advent of the internet and electronic typesetting (like LaTeX), the journals took on a very laborous and difficult job. But now information is primarily disseminated over the internet; authors typeset their own papers; and the cost of publishing (both in print and online) has dropped dramatically.

And this is where the problem begins — even given how much easier it is to publish and distribute information these days, journals frequently cost thousands of dollars per title per year. For example, Elsevier-published journals cost an average of $6,598 a year. Elsevier’s profits, on the other hand, are upwards of $1,000,000,000.00 annually. Yes, that is one billion dollars. Not bad for a company that is outsourcing most of their work to academic volunteers! Plus, they get to keep the copyright to the journals to boot — often keeping extremely strict rules about where and how authors are allowed to distribute their own papers, meaning that most scientists cannot submit a paper to be published in a journal *and* make it freely available to the scientific community.

So why does the scientific community continue to participate in this system? Prestige. Journals are essentially ranked — certain journals have a reputation of having higher standards or publishing more high-impact work than others; as a result, a publication in a high-ranking journal like Nature can make a researcher’s career (resulting in near-guaranteed admission to graduate school, appointment to a professorship, or even tenure). Without an overhaul of the entire system, and of the scientific community’s perceived value of publishing in reputable journals (often published by companies like Elsevier), many researchers feel that they must ‘publish or perish’.

Current Events

Taking advantage of the aforementioned benefits of electronic dissemination, open access archives of scientific papers such as ArXiv and the Public Library of Science were created to serve as centralized databases of published researcher. These databases got around journal copyrights by serving as databases for ‘pre-print’ papers — essentially rough drafts of papers that were available before the ‘final’ paper was published. In addition to these open access archives, the National Institute of Health formed PubMed, an open-access archive that required all recipients of NIH research grants to submit a copy of their final paper under the belief that publicly-funded research should be publicly-accessible.

However, in December 2011 the Research Works Act was introduced, which would effectively nullify the efforts of the NIH and PubMed. The act prohibits any sort of open access mandate for federally funded work — including the National Institute of Health, National Science Foundation, and Department of Energy (all organizations that offer large grants for scientific research).

The Research Works Act (RWA) caused quite a stir in the scientific community; providing a spark that pushed several researches into action. The Cost of Knowledge was started to spread awareness of the RWA and begin a boycott of all Elsevier-published journals. Amazingly, over 7000 researchers have signed it — refusing to publish in any of Elsevier’s journals, some of which are the aforementioned prestigious journals that can make a career. I am proud to have added my own name to the list — I would love nothing more than to see an end to these ‘closed-access’ publishers that take advantage of the scientific community for large profits.

And this brings the story to the present. It seems that all of the RWA-related noise had an impact — Elsevier withdrew its support for the RWA, and the representatives that originally backed the bill dropped support for it too. For now, it appears that the RWA is dead.

Not only is the RWA dead, but there is now a bill being pushed through Congress — the Federal Research Public Access Act — would require that research funded by eleven federal agencies (see the wikipedia page for a full list) be open access to the public, in a searchable archive similar to arXiv or PubMed. The passing of this bill would be a huge success for open access, and would make a huge portion of new scientific research (a lot of research gets funded through these federal agencies) available to the public, free of charge.

Take Action

There’s lots that you can do if you’re interested in supporting the FRPAA and want to help end the absurd policies of academic journal publishers. Things that anyone can do:

-Read about the FRPAA; learn about it, and form your own opinion on it!
-Sign a white house poetition to have President Obama review the FRPAA if you want to support it.
-Write a letter to your local representatives asking them to co-sponsor and support the FRPAA!
-Spread the word! After all, we’re looking to improve dissemination of information — tell your friends, discuss it with them, form opinions, and take action!

If you’re working in academia, additional things you can do:
-Refrain from publishing in an Elsevier journal — you can read more (and sign a list of scholars that are boycotting Elsevier) at The Cost of Knowledge.
-John Baez at Azimuth made some sweet posters to place on your office door to raise awareness about the Elsevier Boycott. Print one out and post it on your door!

H@cking Medicine

•1 March, 2012 • 24 Comments

This past weekend, I went to the H@cking Medicine conference at the MIT Media Lab; a conference aimed towards bringing a diverse group of people together to hack at solutions to problems at healthcare. It was a great time, so I decided to blog about my experiences this weekend! The following consists of a combination of my notes (taken during the conference) and my memories, in as close to chronological order as I could determine.

Continue reading ‘H@cking Medicine’

 
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