towards an inexpensive open-source desktop ct scanner _ the tricorder project

18/5/2014 Towards an inexpensive open-source desktop CT scanner | the Tricorder project

http://www.tricorderproject.org/blog/towards-an-inexpensive-open-source-desktop-ct-scanner/ 1/19

Towards an inexpensive open-source

desktop CT scanner

Posted on October 22, 2013

A bit of a story, and then a lot of pictures — by far the most interesting class I’ve ever taken

was Advanced Brain Imaging in grad school. As a hands on lab class, each week we’d have a

bit of a lecture on a new imaging technique, and then head off to the imaging lab where one of

the grad students would often end up in the Magnetic Resonance Imager (MRI) and we’d see

the technique we’d just learned about demonstrated. Before the class I was only aware of the

structural images that most folks think of when they think of an MRI, as well as the functional

MRI (or fMRI) scans that measure blood oxygenation levels correlated with brain activity and

are often used in cognitive neuroscience experiments. But after learning about Diffusion

Tensor Imaging, spin-labeling, and half a dozen other techniques, I decided that the MRI is

probably one of the most amazing machines that humans have ever built. And I really wanted

to build one.

MRI is a spatial extension to nuclear magnetic resonance spectroscopy (NMR), and requires

an extremely homogeneous high-intensity magnetic field to function — far more uniform than

you can achieve with permanent magnets or electromagnets. For MRI, this uniformity is often

http://www.tricorderproject.org/blog/towards-an-inexpensive-open-source-desktop-ct-scanner/

http://www.tricorderproject.org/blog/wp-content/uploads/2013/10/rsz_dsc_0803.jpg

http://en.wikipedia.org/wiki/MRI

http://en.wikipedia.org/wiki/Nuclear_magnetic_resonance_spectroscopy



accomplished using a superconducting magnet that’s cooled to near absolute zero using

liquid helium. This, of course, makes it extremely technically difficult to make your own

system. While folks have been able to use large electromagnets for NMR (they average out

the magnetic field intensity over the sample by spinning the sample very rapidly while it’s

inside the magnet), I haven’t seen anyone demonstrate building an imaging system using an

electromagnet. There are some experimental systems that try to use the Earth’s magnetic

field, but the few systems I’m aware of are very low resolution, and very slow.

Volumetric biological imaging has two commonly used tools — MRI and Computed

Tomography (or CT), sometimes also called Computed Axial Tomography (or “CAT”) scanning

— although ultrasound, EEG, and a bunch of other techniques are also available. Fast forward

about two years from my brain imaging class (to about three years ago), I had started my first

postdoc and happened to be sitting in on a computational sensing / compressed sensing

course.

http://en.wikipedia.org/wiki/Computed_tomograph

http://en.wikipedia.org/wiki/Compressed_sensing



About the same time I happened to be a little under the weather, and stopped into a clinic. I

thought I’d torn a muscle rock climbing, but after examining me the doctor at the clinic

thought that I might have a serious stomach issue, and urged me to visit an emergency room

right away. As a Canadian living abroad, this was my first real contact with the US health care

system, and as exciting as getting a CT was (from the perspective of being a scientist

interested in medical imaging), from a social perspective it was a very uncomfortable

experience. Without really going into details or belaboring the point, universal health care is

very important to me, and (what many consider) a basic human right that most of the folks in

the developed world have access to. My mom was diagnosed with cancer when I was young,

and we spent an awful lot of time in hospitals. Her and my dad still do, after 15 years and

more surgeries than anyone can count. It’s frightening to think of where we’d all be if her

medical care wasn’t free. And so when a bill showed up a month or so after my emergency

http://www.tricorderproject.org/blog/wp-content/uploads/2013/10/rsz_1dsc_0692-e1382244864549.jpg

http://www.theatlantic.com/international/archive/2012/06/heres-a-map-of-the-countries-that-provide-universal-health-care-americas-still-not-on-it/259153/



room visit for nearly $5,000 (most of which was covered by a health insurance company), I

nearly needed a second trip to the emergency room, and I thought a lot about the many folks I

knew, including my girlfriend at the time, who didn’t have any form of health insurance and

basically couldn’t go to the doctor when they were ill for fear of massive financial damage.

With all of this in mind, knowing the basics of medical imaging, and having just discussed

computed tomography and the Radon transform in the class I was sitting in on, I decided that

I wanted to try and build an open source CT scanner, and to do it for a lot less than the cost

of me getting scanned, by using rapid prototyping methods like laser cutting and 3D printing.

It’s been a few years since I’ve had access to a laser cutter, and they’re one of my favorite

and most productive rapid prototyping tools. In the spirit of efforts like the Reprap project, I

enjoy exploring non-traditional approaches to design, and designing machines that can be

almost entirely 3D printed or laser cut. Fast-forward almost two and a half years to last

month, and the local hackerspace happened to have a beautiful laser cutter generously

donated. This is the first cutter I’ve had real access to since grad school, and with the CT

scanner project waiting for a laser cutter and a rainy day for nearly two years, I immediately

knew what I wanted to have a go at designing. On to the details.

From a high-level technical standpoint, a computed tomography or CT scanner takes a bunch

of absorption images of an object (for example, x-ray images) from a variety of different

angles, and then backs out 3D volumetric data from this collection of 2D images taken from

different angles. In practice, this is usually done one 2D “slice” at a time, first by rotating an x-

ray scanner around an object, taking a bunch of 1D images at tens or hundreds of angles, and

then using the Radon transform to compute a given 2D slice from this collection of 1D images.

http://en.wikipedia.org/wiki/Radon_transform




One can then inspect the 2D slices directly to see what’s inside something, or stack the

slices to view the object in 3D.

Mechanically, this prototype scanner is very similar to the first generation of CT scanners. An

object is placed on a moving table that goes through the center of a rotating ring (or “gantry”).

Inside the ring there’s an x-ray source, and on the other side a detector, both mounted on

linear stages that can move up and down in unison. To scan an object, the table moves the

object to the slice of interest, the gantry rotates to a given angle, then scans the source and

detector across the object to produce a 1D x-ray image. The gantry then rotates to another

angle, and the process repeats, generating another 1D image from a slightly different angle.

After generating tens or hundreds of these 1D slices from different angles, one backs out the

2D image of that slice using the Radon transform. The table then moves the object slightly,

and the process is repeated for the next slice, and the hundreds of other slices that are often

taken in a medical scan. Modern scanners parallelize this task by using a fan-shaped beam

of x-rays and hundreds of simultaneous detectors to scan someone in about a minute, but the

first generation of scanners could take several minutes per slice, meaning a scan with even

tens of slices could take an hour or more.




Designing an almost entirely laser-cuttable CT scanner with four axes of motion, one being a

large rotary gantry, was a lot of fun and an interesting design challenge. I decided that a good

way to rotate the gantry would be to design it as a giant cog that sat atop a system of drive

and idler cogs, that could slowly index it to any angle.

One of the issues with laser cutting a giant cog is finding something to mate with it that can





transfer motion. I’ve press-fit laser cut gears onto motor shafts before (like with the laser cut

linear CNC axis, but in my experience they can slip or wear rather quickly, and I like being

able to disassemble and reassemble things with ease. I decided to try something new, and

designed a laser-cuttable 2.5D timing pulley that mates with the main rotary cog, and

securely mounts on a rotary shaft using a captive nut and set screw. On either side of the

shaft there’s space for a bushing that connects to the base, and inside the base there’s a

NEMA17 stepper from Adafruit that transfers motion to the drive shaft using a belt and timing

pulleys.

A small lip on the base acts as the other edge of the timing pulley, and helps keep the main

rotary axis aligned.

http://www.thingiverse.com/thing:3554

http://www.adafruit.com/products/324




Inside the rotary gantry are two linear axes 180 degrees apart — one for the source and the

other for the detector. The gantry is about 32cm in diameter, with the bore about 15cm, and

the gantry itself is about 8cm thick to contain the linear axes.

Each linear axis has a small carriage that contains mounts for either the source or detector,

some snap bushings for two aluminum rails, and a compression mount for the timing belt.





Each axis also has an inexpensive NEMA14 stepper and an idler pulley. Here, I’m using a

very small solid state high-energy particle detector called the Type-5 from Radiation Watch,

which can be easily connected to an external microcontroller. This is really very easy to work

with, and saves me from having to use a photomultiplier tube and scintillation crystal that I

found on eBay from an old decommissioned PET/CT scanner.

I’m certain if the symmetry were any more perfect, it would move one to tears. The rotary

gantry has to be symmetric to ensure proper balance and smooth rotation. After rotating the

gantry 180 degrees, here you can see the other linear axis intended for the source. It currently

just contains a mount pattern with 4 bolts, that a source will eventually mount to.

Safety is very important to me. In medical diagnostic imaging it’s often important to have an

image as soon as possible, but that’s not the case for scanning non-living objects purely for

scientific or educational interest. This chart from XKCD shows the radiation that folks typically

absorb from every day adventures like banana-eating and sleeping beside someone to hopping

on planes or having a diagnostic x-ray. I’ve designed this scanner to operate on levels slightly

above the natural background level, well into the blue (least intense) section of the xkcd

graph, and make use of a “check source”, which is an extremely low intensity source used to

verify the functionality of a high-energy particle detector. The trade-off for this safety is

acquisition time, and it will likely take a day or more to acquire data for even a small object.

This aspect of the design is scalable, such that if the scanner were to be used in a research

environment in a shielded room, folks braver than I should be able to acquire an image a good

deal faster.

https://www.inventables.com/technologies/smooth-idler-wheel-kit

http://www.radiation-watch.org/p/english.html


http://xkcd.com/radiation/



The sandwich of four plates on either end of the linear axes contain precision mounts for the

aluminum shafts, as well as a setscrew with captive nut to hold the shafts in place.

The table itself is about 40cm long, and offers nearly 30cm of travel. It uses a light-weight

nylon lead screw to index the table, with a NEMA14 drive motor located in the base.





To test out the motion and detector, I put together an Arduino sheild with a few Pololu stepper

controllers and a connector for the detector. The seeed studios prototype board I had on hand

only had space for three stepper controllers, but it was more than enough to test the motion.

Each axis runs beautifully — I was sure the rotational axis was going to have trouble moving

smoothly given that most of the moving parts were laser cut, but it worked wonderfully on the

first try, and moves so fast I had to turn down the speed lest the neighbours fear that I was

building a miniture Stargate…

When I solidify all the bits that have to be in the controller, I’ll endeavor to lay out a proper

board much like this prototype, but with four stepper controllers, and an SD card slot to store

the image data for long scans.


http://www.pololu.com/catalog/category/120



For size, here you can see the Arduino and shield together on the scanning table. I’m hoping

to start by scanning a carrot, move up to a bell pepper (which has more non-symmetric

structure), and work up to an Apple. Since time on commercial machines is very expensive, I

think one of the niche applications for a tiny desktop CT scanner might be in time-lapse scans

for slowly moving systems. If the resolution and scan speed end up being up to the task, I

think it’d be beautiful to plant a fast-sprouting seed in a tiny pot and continually scan it over a

week or two to build a 3D volumetric movie of the plant growing, from watching the roots in the

pot grow, to the stalk shooting up and unfurling its first leaves. I’m sure the cost of generating

that kind of data on a medical system would be astronomical, where the material cost of this

prototype is in the ballpark of about $200, although I’m expecting that a source will add about

$100 to that figure.




13 THOUGHTS ON “TOWARDS AN INEXPENSIVE OPEN-SOURCE DESKTOP CT SCANNER”

Share this:

And finally, here’s a quarter-size acrylic prototype that I designed and cut in an afternoon a

few weekends ago, that started the build and brainstorm process. My recently adopted rescue

cat ironically loves to hang around the “cat” scanner, and has claimed nearly all of the open

mini spectrometers I’ve built as toys to bat around…

Laser cutters are really amazing machines, and it’s really incredible to be able to dream up a

machine one morning, spend an afternoon designing it, and have a moving functional

prototype cut out and assembled later that evening that you can rapidly iterate from. Since

laser cutters are still very expensive, this work wouldn’t have been possible without kind folks

making very generous donations to my local hackerspace, and I’m extremely thankful for their

community-minded spirit of giving.

thanks for reading!

This entry was posted in Uncategorized and tagged openct by peter. Bookmark the

permalink [http://www.tricorderproject.org/blog/towards-an-inexpensive-open-source-

desktop-ct-scanner/] .

Email Facebook 1K+ Twitter 176 Reddit Digg

Google

http://www.tricorderproject.org/blog/towards-an-inexpensive-open-source-desktop-ct-scanner/?share=email&nb=1

http://www.tricorderproject.org/blog/towards-an-inexpensive-open-source-desktop-ct-scanner/?share=facebook&nb=1

http://www.tricorderproject.org/blog/towards-an-inexpensive-open-source-desktop-ct-scanner/?share=twitter&nb=1

http://www.tricorderproject.org/blog/towards-an-inexpensive-open-source-desktop-ct-scanner/?share=reddit&nb=1

http://www.tricorderproject.org/blog/towards-an-inexpensive-open-source-desktop-ct-scanner/?share=digg&nb=1

http://www.tricorderproject.org/blog/towards-an-inexpensive-open-source-desktop-ct-scanner/?share=google-plus-1&nb=1

http://www.tricorderproject.org/blog/wp-content/uploads/2013/10/1264585_4716534411740_673623925_o.jpg

http://www.tricorderproject.org/blog/?p=206

http://www.xerocraft.org/

http://www.tricorderproject.org/blog/category/uncategorized/

http://www.tricorderproject.org/blog/tag/openct/

http://www.tricorderproject.org/blog/author/peter/

http://www.tricorderproject.org/blog/towards-an-inexpensive-open-source-desktop-ct-scanner/



BlackHawk

on October 24, 2013 at 9:46 am said:

Hi! very nice project!

I am a future radiologist and quite interested on this kind of topics.. some questions

for you:

1) you say you use very low radiation, could you bee more precise?

2) this prototype makes DICOM images already?

thank you!

peter

on October 24, 2013 at 1:08 pm said:

Thanks!

I have a 1uCi Cadmium-109 check source on its way (as well as a pound of

lead shielding to help put together a rough collimator). Cd-109 is the lowest-

energy radioisotope that I could find, that emits around 22keV if I remember

correctly — which is absorbed about 50% by 2cm of tissue, so I think there

should be usefully contrastive absorption for things like vegetables. I was also

considering a Barium-133 source, which is higher energy (80-120keV, I think),

so perhaps more suitable for things that have some small amount of metal,

but Ba-133 is not monochromatic. These radioisotope check sources are

sealed in epoxy, and are of such low intensity that they’re not licensed,

generally considered pretty safe unless you eat them or tape them to your

body for long periods, and can apparently be disposed of in the trash.

In order for the imaging to work, the source has to be completely shielded

such that it only emits in about a 1-2mm dia cylinder outward, facing the

detector — something like the shape of an uncooked noodle of spaghetti. This

dramatically reduces the intensity of an already very low intensity source. If

the numbers I’ve read are correct, this should give around one high energy

photon per second in that 1mm cylinder to the detector at 30cm away, and

zero everywhere else. That should give a signal-to-noise ratio of about 10:1 if

you sample each point for a minute, as background is about 5 counts per

minute on my desk. Hopefully that will be enough to give an okay image.

So, to answer your question, the radiation level should be zero above

http://www.tricorderproject.org/blog/towards-an-inexpensive-open-source-desktop-ct-scanner/comment-page-1/#comment-226

http://www.tricorderproject.org/




background outside of the bore, and so slightly above background in an area

the size of a spaghetti noodle within the bore that you could measure it in

bananas-worth of exposure. The trade off is of course extremely long imaging

times.

james1095

on November 20, 2013 at 11:31 pm said:

Having had a fair amount of experience working on/with dental and

veterinary xray machines, I think you’ll find that a small radioactive

check source is woefully inadequate for any kind of imaging. The

intensity drops with the inverse square of the distance and more than a

few inches away you’re not much above background levels. You

*might* get a vaguely recognizable image with a source to sensor

distance of an inch or two, an extremely sensitive sensor and a very

long exposure but it will be extremely challenging to get a usable

signal to noise ratio.

Realistically a dental xray head is the bare minimum for useful xray

imaging. A dental tube run at a few mA coupled with an intraoral digital

xray sensor ought to make for an acceptable desktop CT scanner but

you will want to be careful with the shielding. The heads themselves

are very well shielded but there will be some scatter and you will have

to be very careful to block the beam behind the sensor. There are

some very real safety considerations but anything powerful enough to

create an image will be powerful enough to be hazardous.

programmer1200


Wow great work and really cool right up! Any chance of seeing a video of it working?

peter








Thanks! Once the source arrives and it’s generating images, I definitely plan

on making a video. The operational part will have to be a time lapse, perhaps

even over days! Can you imagine taking a CT of a bell pepper that takes so

long that it wilts while you’re scanning it? In your data, one side of the pepper

might look young, and the other might look wilted. And I don’t think there’s

enough room in my fridge for a CT scanner…

thedeepfriedboot


Could could try to install it in Steve’s BarBot and see if he notices. He

already has a RPi in there that could run it.

Barney


Great project!

Could it be used for reverse engineering of products as well to create digital models of

physical forms? As 3d Scanners are used for now but a lot more cost effective…

Will you be sharing the source any time soon? I’d love to have a play with it myself

peter


Thanks! In theory you could use a CT to make extremely accurate volumetric

3D renderings of an object — much more than just the surface, you’d sample

the inner volume as well. In practice, with this machine operating just above

the background SNR, it will likely take many hours per slice for an apple-sized

object, so likely several days for a bunch of slices. That being said if it was

modified by folks with much more radiography safety experience than myself

to include a much more intense source, and installed into a shielded

environment, it’s theoretically possible that you could bump up the source







intensity to make scans much quicker. Alternatively, if someone were to

design an inexpensive 1D linear radiation detector about 15cm long with (say)

100 or more pixels, then you could acquire the projections for one rotation all

in parallel, and eliminate the need for mechanical scanning inside the gantry.

This is the acquisition method of the current generation of CT scanners, where

they use a fan-beam of x-rays to reach all the detectors simultaneously.

I am definitely planning on releasing the source shortly, after I’ve had the

chance to put together the proper Arduino shield (half done, I worked on it a bit

last night), make some small changes to the design for neater cabling, limit

switches, and such, as well as (hopefully) acquire the first images when the

source arrives. With any luck it’ll show up sometime this week! I also have to

consider how to deal with the safety aspects — having a background in

physics and a bit of medical imaging I’m fairly comfortable with this, but I’d

feel very uncomfortable for folks without a good background in science and

radiology and a deep understanding and respect for radiological safety building

their own. Then again the source will likely be undetectable even a few feet

away, so perhaps I’m being overcautious, but it’s best to err on the side of

caution.

That being said, I’m excited about what folks might want to do with a generic

low-cost platform for computed tomography. If it makes it incredibly easy for

someone to stick on a terahertz source and detector and make a terahertz CT

scanner, for example, that would make me very excited.

tekvax


have you seen this?

http://benkrasnow.blogspot.ca/2013/01/diy-x-ray-ct-scanner-controlled-by.html

peter


Yes,, and it frightened me senseless. I also would have thought that you’d

need a license and proper shielding for such an intense x-ray source.


http://benkrasnow.blogspot.ca/2013/01/diy-x-ray-ct-scanner-controlled-by.html





programmer1200

on January 3, 2014 at 3:51 pm said:

Any updates ?(Sorry ,I’ve been going to your site like every week hoping for an

update)

peter

on January 3, 2014 at 5:28 pm said:

Sorry to be slow with updates, it’s been a busy few months!

1) 1uCi Cadmium-109 source arrived, which primarily emits 22keV photons, for

which the detector should be ~30% efficient. I observed a factor of ~2200x

less detections than I was expecting, and posted the data on the

manufacturers forum. They said the detector’s threshold is calibrated for

Cesium (88keV emissions), and I need to verify the detections for the 22keV

photons are present on a scape then swap out some resistors. The number of

detections that I’m seeing is on par with Cadmium-109′s few ~>88keV

emissions, suggesting that’s the case.

2) I gave away my old oscilloscope a while ago to make room for a move, so a

bunch of us down at the hackerspace have ordered a proper one that should

be here shortly, if it hasn’t already arrived (I just returned from the holidays).

That means I’ll be able to do the verification and swap out the resistors

shortly. I may also end up moving the source and detector to the inside of the

ring, rather than the outside — that will shorten the distance between them

from 30cm to 15cm.

3) While this has all been going on in the background, I completely redesigned

the Mark 5 Science Tricorder to remove the Gumstix due to wifi issues, and all

the parts came in while I was on holidays. I started assembly last night, and

I’ll be making more posts about it shortly as it comes together!






ksaiyo

on April 8, 2014 at 1:37 pm said:

Saw the article in Make: Volume 38. Quite interested in the project. I would like to see

what could be done with a more powerful X-ray source. I have seen projects where an

X-ray source and phosphorescent screen are held stationary, and the object is rotated

with a step motor and a digital photo is taken of the screen. Software is used to build

a the 3D image, but the images tend to have a lot of artifacts. I am looking forward to

your first images.


towards an inexpensive open-source desktop ct scanner _ the tricorder project

Documents

brain imaging class

imaging lab

diffusiontensor imaging

imaging system

new imaging technique

tricorder projecthttp

magnetic resonance imager

volumetric biological