So yesterday afternoon, I was sitting next to my good friend Tim and half-listening to a talk at BarCamp (half listening, half writing a talk I was giving right after the one I was listening to).
The talk was by Saya, and she mentioned that she wanted a boyfriend who smells of campfires.
I stopped working on my slides and raised my hand.
-all the time?
-yes.
Tim raised his hand.
-even right after a shower?
-yes, right out of the shower.
I looked at Tim and said “I’m sure I can make that scent, let’s try it!”
I’m happy to announce the formation of a new Open Science group here in Chicago, called ChiOpenSci. We’re open to enthusiasts, amateurs, researchers, hobbyists, anyone interested in solving scientific problems using (and making) open source and open culture tools and philosophy.
First meeting will be on Sunday, September 12 at 4pm at Pumping Station: One in Chicago 3354 N. Elston Ave.
Feel free to bring your enthusiasm and ideas for problems that are best tackled via open software style approaches. Also, all realms of science that study natural phenomena are welcome: astronomy, physics, chemistry, biology, math, engineering, and many more I’m sure I haven’t mentioned.
I just completed a new (much better) scanning head in preparation for final build and testing, but how do you know if the head is actually moving back and forth?
The answer I came up with is to use reflected laser light to amplify the movement of the scanning head.
To test the new head, I mounted a small mirror (actually a sequin, they’re lighter) in the needle mounting point, shined (shone?) a laser at the mirror to see if I could see movement in the reflected laser point as the scanning head moves back and forth. What I saw was a little movement, but the laser reflection was so diffuse and the movement was so much smaller than the laser reflection that the movement didn’t show well on the video I shot, so you’re going to have to put up with still photos until I acquire better mirrors and/or a more focused laser.
When I first mentioned I was going to demo the early prototype of the STM at the Open Science Summit, everyone who had actually seen the thing asked me (worriedly) how I was going to get it through the security checkpoints at the airport.
Looking for advice, I brought the prototype to Steve Y., the experienced head of security at my office, and asked what he thought I should do. “Well, what you have here doesn’t look great, but it’s not bad. Here’s what I’d do: put it in a nice box, put some official labels on there, put some kind of identifying label on there, and then send it through the X-ray machine alone. You’ll be fine.” With this pattern to follow, here’s what I did:
I’m working to get the STM working as fast as possible, but it’s not 100% – I’ve got basic functionality tested and working, but no images yet – I’m hoping to have images within a month or so.
Current work:
A new scanning head
Complete the mechanical supports and approach mechanism (current state photo of the mechanicals, above)
Programming the arduino and the python script that gathers the image data
Final electronics testing
Getting everything prepared for air flight (expect a post in the near future on preparing electronics for TSA inspection)
Here is a video of my latest tests – the digital side talking to the analog side and driving the scanning head (faintly):
If that’s not enough for you, here is some good background info to read about STMs:
In case you missed the youtube video, the STM is now electronics hardware complete – well, I have a very small change coming in the mail (a two-in-one DAC chip) to replace the two separate DACs. This may improve the code efficiency slightly, but I’m going to wait a while before I implement the change.
I’m working on the programming right now, and not sleeping much while I do because (see below)…
I have been invited to display the STM at the Open Science Summit in Berkeley at the end of the month. If you’re there, stop by the Berkeley International House and say hello – I’ll be at the hardware tables.
I’ve been wanting to upgrade the storage in ChemHacker central for a while – but I haven’t found a good, sturdy storage unit that is large, can handle holding a lot of weight, and is chemically resistant.
Until now.
I found this old Faygo-labeled shelving unit in a nearby alley:
After a (lot of) cleaning, here it is holding tools and a wide assortment of chemicals in the underground ChemHacker Lab:
As I mentioned earlier, I’m working on programming an arduino interface for the ChemHacker STM.
The arduino currently has to handle the following tasks:
serial control of the five digital potentiometers (amplifier gain control)
serial control of the 24 bit DAC (signal input to the microscope)
analog signal processing from the microscope (via built-in ADC lines)
serial data to the computer of the scanned data (for image processing)
A future task for the arduino may be:
automated control of a stepper motor (for sample approach and control)
My road map for programming is as follows:
establish serial control of the potentiometers
establish serial control of the DAC
establish signal into the ADCs
establish serial data line to computer (and figure out some kind of live image processing system)
interface with microscope circuit(s)
establish stable scanning
As always, things take more time than you think – I foolishly thought I could get steps 1 and 2 done in a few weeks. After nearly a month of struggling, I finally have (1) accomplished, and with some help from some excellent electronic engineers, I’m quickly closing on (2).
Many many thanks to all the people who publish their SPI code on various Arduino boards, without your examples, I never would have gotten this far…
Here’s what I’ve learned from weeks of banging my head into walls: the entire SPI setup must be used for the arduino’s SPI to activate – that includes declaring pins you don’t intend to use (like the MISO and the SLAVESELECT)
A quick update on where the ChemHacker STM project stands: I’ve completed assembling the electronic components and I’m moving to programming the arduino (well, that’s actually a sanguino in the photo, but I’m moving the whole project to arduino duemilanove based hardware).
What you see in the photo is the red sanguino microcontroller, the green main amplifier board, the tan tunneling current amplifier, and on the breadboard are the digital pots and 24bit DAC I’m using for controlling the microscope. At the top right is the microscope nanopositioning head.
The end result of this project will be an open source STM with modern electronic controls.
I’m happy to announce the formation of a new Open Science group here in Chicago, called ChiOpenSci. We’re open to enthusiasts, amateurs, researchers, hobbyists, anyone interested in solving scientific problems using (and making) open source and open culture tools and philosophy.
