Arduino Spectrophotometry

Well, OK, just measuring ambient light for now… but we’ll get there in class soon.

Students in my Computational Methods class are using an Arduino to do some simple sensor measurement stuff. I found a bunch of old FSRs and photoresistors in a bin in the lab. No markings so no datasheets.

No worries –

A little Mathematica “Connected Device” stuff to talk to the Arduino, my interface to Argyll CMS to talk to the i1 Pro, and adjusting the blinds in my office …

DeviceReadTimeSeries + getAmbient = profit$

Pretty linear… We’re ready to roll.

TAPASI – Monkeys and Microstimulation

I’m not sure if ‘A’ and ‘D’ are smoking 

Some monkeys and some microstimulation.

Courtesy of Gabe Diaz, a little scene from Graziano, Taylor and Moore, 2002. Dots indicate trajectory of the left arm after microstimulation of the right hemisphere PFC. Remember kids – PFC does everything!

But seriously, it’s a neat paper and there are more fun images, more than can possibly fit in The Archives™

Wasting Time – TheraPutty

Yes, so many other things I could be doing, but this is more important – using a webcam, some Mathematica, and therapy putty.

Somehow, as I age, I keep accidentally hurting myself. I know, weird right? So, while doing some he-man building things (putting a keyboard tray on my standing desk qualifies, right?) I accidentally wrenched my elbow while using a drill-driver, resulting in so-called “golf elbow” (similar to its tennis cousin, just the other tendon). 

Beth had some TheraPutty and I noticed that doing certain exercises with it seemed to help. That and Ibuprofen I suppose. I took two tubs, blue – stiff, and yellow – soft, to the lab to fondle while working. 

After about a week, I noticed that the blue, which was supposed to be super resistant, had softened to be almost as soft as the yellow. It was pretty strange: was I really ‘working it’ that much that I was able to break down seriously viscous rubber and other miscellaneous plasticizers with my bare brutish hands?

I fired off an email to the company that manufactures it, Fabrication Enterprises, Inc, down in White Plains. I wasn’t really expecting a response, I was just curious. 

I had my Ziggi camera sitting on my desk since I had just finished teaching. So, I decided to roll up the yellow and blue and do a time lapse of them ‘settling’ since that would be a relatively good estimate of their relative viscosity. A little Mathematica image processing to find the individual balls in the image, segment and measure them, and I ended up the following:

Procrastination, quantified.

Sure enough, they spread out at almost exactly the same rate (the little glitch out around 5 minutes is where I had to re-start the image acquisition because, well, I really wasn’t being a good scientist, was I?). And pretty much ended up at exactly the same size after about 5-6 minutes. I wanted to go home and eat dinner, so I stopped the experiment — science has to eat.

Lo and behold, today I got a very nice email from Jason Drucker, Senior Vice President of Sales and Marketing at FEI. He apologized for taking time to get back to me, but, as it turned out he had sent my question to the senior manufacturing chemist for comment! That’s wonderfully nuts- and indeed, she/he replied:

I have never heard of the blue putty getting soft after using it for a long period of time. In fact, so soft that the yellow is firmer in viscosity. The only way this can happen is the putty was exposed to one of the following, alcohol, cleaning fluids, hand creams or any solvents. These ingredients help breakdown the silicone polymer. Once broken down the putty will become softer.

Chief Chemist- FEI

Guess what — I was in the lab with the blue and cleaned up some of the 3D printer resin, using the only thing that works, isopropyl alcohol, 99%. I almost certainly had some on my hands at some point and totally destroyed my blue putty. 

So, my bad, and let this be a lesson to you. If you’d like the images and the Mathematica, you can grab it here. Let me know if you play around with it. May your procrastination be fruitful.

The Archives of Potentially Amusing Scientific Images (TAPASI)

Wherein serious but silly scientific images are archived.

A few months ago, I was having lunch with Sarah Creem-Reger at a conference at UofR. Somehow, the conversation got around to publishing and I relayed a story told to me by Irv Biederman about a conflict he had with some JEP editors about a figure he and Maggie Shiffrar wanted to include in a paper. I mentioned that I had a collection of my favorite article illustrations and Professor Creem-Reger asked me about some of my other favorites. This is the story of one such favorite and my offering of more such stories, irregularly, in the future.

The paper in question is about perceptual learning, and the image was ‘modified’ from a 1948 paper on chicken sexing. As it turns out, there are people out there who are really really good at determining the gender of baby chicks by just looking at them. They wanted to figure out how they did it (they did, read the paper), if it could be easily taught (it seems like it), and if it generalizes to other sorts of tasks (again, depending).

The caption from the Biederman & Shiffrar paper reads —

An accepted grasp for chick sexing. (Modified from “Chick Sexing” by J. H. Lunn, 1948, American Scientist, 36, pp. 280-287. Copyright 1948 by the American Scientist Photograph by the University of Minnesota Photographic Laboratory. Adapted by permission.)

The original image from Lunn (1948) shows the ‘correct hand grip for chicken sexing’, before adaptation —

How to hold a chick for proper sexing.

and Irv and Maggie’s adaptation includes a bar over the eyes of the baby chick to preserve the anonymity of the fondled fowl —

Anonymized chick.

Apparently the editors of JEP:LMC lacked a proper sense of humor or perhaps an overly serious position on humor in science. Thus, they did not want to publish the modified version (note that the peer review of the science found the work well done and relevant / interesting to the field)

An update from Irv —

 It wasn’t the editor(s) of JEP: L, M, & C that stirred a bit. Roddy Roediger (the Editor) and the reviewers had no problem whatsoever with the photo. It was a woman from APA who called (perhaps from APA’s central publications office) asking me if I wanted the picture published as it was submitted. Of course I said “Yes, that I had put the black bar there.” I never pressed her as to her reason for calling. It was an era where some were confusing sex with sexist and, if memory serves, she might have voiced a vague phrase or two along those lines but perhaps felt that she did not have a winning hand (it was chickens!) and let the matter go.

This resulted in the publication of this, my favorite potentially silly scientific image. Irv and Maggie have done so much important work over the years and I encourage you to check them out. I can also assure you that Irv’s sense of humor remains unscathed.

More soon…

NB – I plan on adding items from my ‘silly images’ folder irregularly in the coming months. If you have anything that is worthy, please let me know at


Biederman, I., & Shiffrar, M. M. (1987). Sexing day-old chicks: A case study and expert systems analysis of a difficult perceptual-learning task. Journal of Experimental Psychology: Learning, Memory, and Cognition, 13(4), 640–645.

Lunn, J. H. (1948). Chick sexing. American Scientist, 36(2), 280-287.

Publish Magazine — August 1989

A short piece about our wedding announcements, printed on a 100-year-old Heidelberg press via computer graphics.

I posted an interview from fps Magazine a while back, and one of my old Wolfram Era Pals, Paul Abbott, asked about the wedding invitation mentioned in that article. I thought I had a copy somewhere, and, indeed I found it in my well curated ‘archives’ (e.g., a Bankers Box in the basement).

This way I’ll never forget our anniversary.

Turns out, Publish Magazine did a story on the work back in 1989, (written by James A. Martin) designed by me and printed by Julie Holcomb Printers. You can see a PDF of the article here. (Be sure to check out the ad from a very early Casady & Greene and reminisce about Crystal Quest, Conflict Catcher, and friends.)

Publish Magazine, August 1989

Animation Magazine — 1989

Unbeknownst to me until several year later, my dad kept a copy of this in his car to show anyone he ever ran into.

Right after we completed knickknack, Animation Magazine did a story on the animation group at Pixar. We had just won the Oscar for Tin Toy so there was a lot of hype. Alas, we were not nominated. The Academy™ wanted to spread the love around I suppose. We weren’t too hurt — the film got a great reception at SIGGRAPH, there was a lot of very worthy competition that particular year, and I’ve had several people since tell me that it was their favorite of the four ‘early’ shorts (We called the master tape with those on it ‘LRTK‘ – short for “Luxo, Red’s (Dream), Tin (Toy), and knickknack). It really was a fun film. The whole group did everything — story, characters, animation, rendering, catering. That’s why the credits don’t specify any roles.

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Computer Pictures Magazine – Jan 1987

In 1984, I started working at the Ohio State Computer Graphics Research Group on a medical imaging project.

In the same basement box with interview from fps magazine that I posted a bit ago, I found a few other gems. Here’s an article from Computer Pictures magazine that features some of the work we were doing back then.

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fps interview – 1995

Published from 1991-2010, fps was an excellent animation magazine with an impressive cast of regular contributors.

Shortly after I left Pixar in 1992, the publisher Emru Townsend got in touch with Tony Apodaca and me for a long-running email conversation about the early days of making those computer animation things. Over the next few years, Emru, Tony and I exchanged questions and answers over a wide range of topics surrounding computer graphics and animation.

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Why Does the Cortex Reorganize After Sensory Loss?


Investigating the Teleology of Cortical Reorganization

A growing body of evidence demonstrates that the brain can reorganize dramatically following sensory loss. Although the existence of such neuroplastic crossmodal changes is not in doubt, the functional significance of these changes remains unclear. The dominant belief is that reorganization is compensatory. However, results thus far do not unequivocally indicate that sensory deprivation results in markedly enhanced abilities in other senses. Here, we consider alternative reasons besides sensory compensation that might drive the brain to reorganize after sensory loss. One such possibility is that the cortex reorganizes not to confer functional benefits, but to avoid undesirable physiological consequences of sensory deafferentation. Empirical assessment of the validity of this and other possibilities defines a rich program for future research.

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Retina and LGN

A demonstration written in Mathematica to show the interaction of the retina and LGN on the sampling of image information from the eyes.

You can play with the receptive field size to see how the whole “Hybrid Images” thing works. Click on the image to go to the demonstration.

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