measurements Archivi - Paola Elefante

Open Data: CT datasets and prototypes

Paola Elefante — Mon, 22 Feb 2016 18:41:22 +0000

In my research work, I often find it difficult to get datasets for X-ray CT for method validation, neither simulated and real data. Of course, there's the classic Shepp-Logan phantom, but in many cases it would save a lot of work to download datasets to test one's methods. As for my knowledge, there is no broad known repository. In the image processing community there are the classical Lena, Barbara pictures, but I am not aware of similar common testing grounds in the X-ray CT one. In many cases the final goal is to apply the developed methods to a particular application case, so datasets are available from a company or a hospital repository. However, I think it would be useful to have a "middle step" and test on simpler phantoms before getting to the real deal. Many applied mathematicians often stop at this middle step, since going further would be out of scope for them. I hope this collection will be useful to others.

Since 3D printing is quite easy and inexpensive nowadays (can be done even in public libraries often), I used a the free software Autodesk 123D to design some 3D printable prototypes for static and dynamic CT. I am here sharing both the ready-made STL file (ready to be printed) and the 123D-project file, in case someone wants to do some personal edits. Anything can be freely use, just please quote the author and the source.

If you are aware of other open data repositories for CT or would like to share suggestions, feel free to comment below. I will update this post and the shared repositories in the future (last update: Feb 22nd, 2016).

Static CT open data

[real data] Tomographic data of a walnut: open dataset from FIPS, authors are indicated at the webpage.

[real data] 3D printable simple phantom prototype: to test contrast agents, geometry preservation of reconstruction method, how different attenuation values are reconstructed. Please quote the author (Paola Elefante) and the link to this post as a source.

[real data] 3D printable blood vessels prototype: to test a realistic static geometry of blood vessels splitting in capillaries. Please quote the author (Paola Elefante) and the link to this post as a source.

The static CT blood vessels prototype.

Dynamic CT open data

[real data] DirLab repository: a open data repository, mostly for image registration researchers.

[real data] 3D printable dynamic blood vessels prototype: to test a realistic dynamic simulation of blood or fluid flowing. In the featured picture you can spot an old version of this prototype. I made some major edits in the design, but I still did not test it. Please quote the author (Paola Elefante) and the link to this post as a source.

Design of the prototype for 2D dynamic CT.

[simulated data] 2D dynamic "Y-phantom": a binary phantom where meaningful topological changes happen, good for interface detection methods (level-set, etc.).

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The "Helsinki walnut" dataset

Paola Elefante — Mon, 16 Feb 2015 07:05:12 +0000

Our research group has made an open access dataset for image reconstruction available at the following link:

www.fips.fi/dataset.php

The measurement data was collected and documented by K. Hämäläinen, L. Harhanen, A. Kallonen, A. Kujanpää, E. Niemi and S. Siltanen. Our group used the walnut data for testing several tomographic reconstruction algorithms, as you can see in the homepage. You are free to use the dataset for scientific purposes, but please take care to cite the authors.

Have fun reconstructing!

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Getting paid to play with LEGO blocks

Paola Elefante — Tue, 11 Nov 2014 18:31:48 +0000

You know you are working in the right place when you find yourself proudly wandering around your workplace with a full bag of original 80s LEGO blocks. People cannot help but throwing inquisitive looks and you go like "It's SCIENCE.".

Today I had to take some measurements with my colleagues Aki and Alexander in the Physics Department X-ray tomography laboratory. This was a completely new experience for me, having myself the background of a theoretical mathematician. Nonetheless, it was exciting to learn how the collecting data machinery works. LEGO blocks were used in the spirit of what Aki prophetically taught me regarding experimental physics: "Whatever works!". We needed to move the sample during the measurements and we used the blocks to control the shift distance and stability better. Some previous LEGO playing was required in the sake of experimental science.

The sample in the measurement setting.

The microtomography laboratory at University of Helsinki.

A couple of words must be spent regarding the sample. We used the classical "Helsinki walnut"(*). It was a little awkward when I went to the shop to buy only two walnuts. I tried to brag with the cashier "I am gonna X-ray them." but I had the feeling this did not impress her very much. Weird.

The walnut was a brilliant choice of real data for sparse X-ray tomography. It has a good variety of attenuation areas, non-trivial boundaries, and totally looks like a brain. It is an excellent alternative to the classical Shepp-Logan phantom. The walnut dataset is about to become public for the benefit of other researchers (I promise I will spread the news on my blog as soon as it gets published).

Now let's keep fingers crossed that I guessed well the customer's needs with such measurement.

(*) See the paper about sparse tomography by Hämäläinen et al..

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