Dataset Open Access

Cone-Beam Computed Tomography Dataset of a Pine Cone

Alexander Meaney

Summary

This dataset is a collection of X-ray projection images of a pine cone imaged in a cone-beam computed tomography (CBCT) scanner. The dataset also includes a metadata file, specifying the scan geometry and other important scan parameters, and a photograph of the sample.

 

Description

Sample Information

The sample is an open cone of a Baltic pine (Pinus sylvestris), approximately 3 cm in diameter. For the scanning process sticky tack was used to attach the sample to a plastic tube placed into the rotation stage.

Scanner

The measurements were acquired using a cone-beam computed tomography scanner designed and constructed in-house in the Industrial Mathematics Computed Tomography Laboratory at the University of Helsinki. The scanner consists of a molybdenum target X-ray tube (Oxford Instruments XTF5011), a motorized rotation stage (Thorlabs CR1-Z7), and a 12-bit, 2240x2368 pixel, energy-integrating flat panel detector (Hamatsu Photonics C7942CA-22).

Scan Settings

721 X-ray projections were acquired using an angle increment of 0.5 degrees. The X-ray source voltage and tube current were set at 40 kV and 1 mA, respectively. The exposure time of the flat panel detector was set to 1000 ms.

Data Post-Processing

Two correction images were acquired before scanning the sample. A dark current image was created by averaging 100 images taken with the X-ray source off. A flat-field image was created by averaging 100 images taken with the X-ray source switched on with no sample placed in the scanner. After the scan, dark current and flat-field corrections were applied to each projection image using the Hamamatsu HiPic imaging software version 9.3.

Data Format

The X-ray projections are stored in .tif format. The metadata is contained in .txt file with formatting that is both human-readable and machine-readable.

Notes

Due to a slightly misaligned center of rotation in the scanner, the CT reconstructions can appear blurry. It was empirically observed that this problem can be compensated for quite well by shifting each projection left by 5 pixels, using circular boundary conditions, before performing any other operations on the projections.

 

Research Group

This dataset was produced by the Inverse Problems research group at the Department of Mathematics and Statistics at the University of Helsinki, Finland: https://www2.helsinki.fi/en/researchgroups/inverse-problems.

 

Additional Links

This dataset was originally created as part of a tutorial on working with measured X-ray data in computed tomography. A video tutorial on the measurement process can be found on the Inverse Problems Channel on YouTube at https://www.youtube.com/watch?v=CWUomAmUDys.

To get started with the data, we recommend looking at the HelTomo toolbox, specifically created for working with CBCT data collected in the Industrial Mathematics Computed Tomography Laboratory, and available at https://github.com/Diagonalizable/HelTomo

 

Contact Details

For more information or guidance in using these datasets, please contact alexander.meaney [at] helsinki.fi.

Files (4.2 GB)
Name Size
20201118_pine_cone_.txt
md5:99187a8f14322776414075decd6d2abb
729 Bytes Download
20201118_pine_cone_collage_fips.png
md5:96472b42b89abfcf12f3c02faafcb757
1.3 MB Download
20201118_pine_cone_projections_1.zip
md5:dbb8fb04d02d168b938a78917d960b88
585.5 MB Download
20201118_pine_cone_projections_2.zip
md5:5952a896972380548970e099ccc8691c
585.6 MB Download
20201118_pine_cone_projections_3.zip
md5:8d897951fba0a213e4b9a16d8dc4ee12
585.8 MB Download
20201118_pine_cone_projections_4.zip
md5:b7f151585f09d8d41e01392315c1d8c4
586.2 MB Download
20201118_pine_cone_projections_5.zip
md5:42951c3dad2b08f8eb63704bbfbd36ab
586.8 MB Download
20201118_pine_cone_projections_6.zip
md5:3ac8f1aed302963c400a74844bc07259
587.0 MB Download
20201118_pine_cone_projections_7.zip
md5:403f398c8fb032daae374e48f0f89cc1
586.2 MB Download
20201118_pine_cone_projections_8.zip
md5:4771e13f20f1eaff60e4c6b929f3d383
122.9 MB Download
20201118_pine_cone_sample.png
md5:583e83a76215ddc165fef31d1a00455b
342.3 kB Download
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