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Radiation dose optimized lateral expansion of the field of view in synchrotron radiation X-ray tomographic microscopy.

Haberthür D, Hintermüller C, Marone F, Schittny JC, Stampanoni M - J Synchrotron Radiat (2010)

Bottom Line: On the contrary, an extension of the field of view in the perpendicular direction is non-trivial.The acquisition protocol can be tuned as a function of the reconstruction quality and scanning time.The method has been successfully applied for the three-dimensional imaging of entire rat lung acini with a diameter of 4.1 mm at a voxel size of 1.48 microm.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Anatomy, University of Bern, Switzerland. haberthuer@ana.unibe.ch

ABSTRACT
Volumetric data at micrometer level resolution can be acquired within a few minutes using synchrotron-radiation-based tomographic microscopy. The field of view along the rotation axis of the sample can easily be increased by stacking several tomograms, allowing the investigation of long and thin objects at high resolution. On the contrary, an extension of the field of view in the perpendicular direction is non-trivial. This paper presents an acquisition protocol which increases the field of view of the tomographic dataset perpendicular to its rotation axis. The acquisition protocol can be tuned as a function of the reconstruction quality and scanning time. Since the scanning time is proportional to the radiation dose imparted to the sample, this method can be used to increase the field of view of tomographic microscopy instruments while optimizing the radiation dose for radiation-sensitive samples and keeping the quality of the tomographic dataset on the required level. This approach, dubbed wide-field synchrotron radiation tomographic microscopy, can increase the lateral field of view up to five times. The method has been successfully applied for the three-dimensional imaging of entire rat lung acini with a diameter of 4.1 mm at a voxel size of 1.48 microm.

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Workflow of a wide-field scan. The images show a rat lung sample from a Sprague-Dawley rat, obtained 21 days after birth, scanned with the acquisition protocol B (Table 1 ▶). (a) Three corrected and independently acquired projections from subscans s                  1–s                  3 are shown. Each one is 1024 × 1024 pixels large and covers a field of view of 1.52 mm. Subscans s                  1 and s                  2 overlap by 141 pixels (red and green overlay), subscans s                  2 and s                  3 overlap by 138 pixels (blue and yellow overlay). (b) Merged projection obtained from the three subscans shown in subfigure (a). Each merged projection has a size of 2792 × 1024 pixels. Owing to the overlap required to merge the projections, the width of the merged projections is slightly smaller than three times the width of the subscans. (c) Cropped slice of the reconstructed tomographic dataset. The dashed red circles mark the start and end of the overlap region.
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fig4: Workflow of a wide-field scan. The images show a rat lung sample from a Sprague-Dawley rat, obtained 21 days after birth, scanned with the acquisition protocol B (Table 1 ▶). (a) Three corrected and independently acquired projections from subscans s 1–s 3 are shown. Each one is 1024 × 1024 pixels large and covers a field of view of 1.52 mm. Subscans s 1 and s 2 overlap by 141 pixels (red and green overlay), subscans s 2 and s 3 overlap by 138 pixels (blue and yellow overlay). (b) Merged projection obtained from the three subscans shown in subfigure (a). Each merged projection has a size of 2792 × 1024 pixels. Owing to the overlap required to merge the projections, the width of the merged projections is slightly smaller than three times the width of the subscans. (c) Cropped slice of the reconstructed tomographic dataset. The dashed red circles mark the start and end of the overlap region.

Mentions: Fig. 4(a) ▶ shows corrected projections from three overlapping subscans prior to merging, including regions where the subscans are overlapping. Fig. 4(b) ▶ shows one merged projection prior to reconstruction and Fig. 4(c) ▶ shows one slice of the reconstructed dataset. The example shown in Fig. 4 ▶ was obtained using the highest number of projections and is therefore protocol B. One reconstructed slice covers a field of view of 2792 × 2792 pixels (4.13 × 4.13 mm), which is almost three times the size of what can be achieved with one single-binned scan (1024 pixels or 1.52 mm). The dashed circles on the reconstructed slice mark the start and the end of the overlap region.


Radiation dose optimized lateral expansion of the field of view in synchrotron radiation X-ray tomographic microscopy.

Haberthür D, Hintermüller C, Marone F, Schittny JC, Stampanoni M - J Synchrotron Radiat (2010)

Workflow of a wide-field scan. The images show a rat lung sample from a Sprague-Dawley rat, obtained 21 days after birth, scanned with the acquisition protocol B (Table 1 ▶). (a) Three corrected and independently acquired projections from subscans s                  1–s                  3 are shown. Each one is 1024 × 1024 pixels large and covers a field of view of 1.52 mm. Subscans s                  1 and s                  2 overlap by 141 pixels (red and green overlay), subscans s                  2 and s                  3 overlap by 138 pixels (blue and yellow overlay). (b) Merged projection obtained from the three subscans shown in subfigure (a). Each merged projection has a size of 2792 × 1024 pixels. Owing to the overlap required to merge the projections, the width of the merged projections is slightly smaller than three times the width of the subscans. (c) Cropped slice of the reconstructed tomographic dataset. The dashed red circles mark the start and end of the overlap region.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2927902&req=5

fig4: Workflow of a wide-field scan. The images show a rat lung sample from a Sprague-Dawley rat, obtained 21 days after birth, scanned with the acquisition protocol B (Table 1 ▶). (a) Three corrected and independently acquired projections from subscans s 1–s 3 are shown. Each one is 1024 × 1024 pixels large and covers a field of view of 1.52 mm. Subscans s 1 and s 2 overlap by 141 pixels (red and green overlay), subscans s 2 and s 3 overlap by 138 pixels (blue and yellow overlay). (b) Merged projection obtained from the three subscans shown in subfigure (a). Each merged projection has a size of 2792 × 1024 pixels. Owing to the overlap required to merge the projections, the width of the merged projections is slightly smaller than three times the width of the subscans. (c) Cropped slice of the reconstructed tomographic dataset. The dashed red circles mark the start and end of the overlap region.
Mentions: Fig. 4(a) ▶ shows corrected projections from three overlapping subscans prior to merging, including regions where the subscans are overlapping. Fig. 4(b) ▶ shows one merged projection prior to reconstruction and Fig. 4(c) ▶ shows one slice of the reconstructed dataset. The example shown in Fig. 4 ▶ was obtained using the highest number of projections and is therefore protocol B. One reconstructed slice covers a field of view of 2792 × 2792 pixels (4.13 × 4.13 mm), which is almost three times the size of what can be achieved with one single-binned scan (1024 pixels or 1.52 mm). The dashed circles on the reconstructed slice mark the start and the end of the overlap region.

Bottom Line: On the contrary, an extension of the field of view in the perpendicular direction is non-trivial.The acquisition protocol can be tuned as a function of the reconstruction quality and scanning time.The method has been successfully applied for the three-dimensional imaging of entire rat lung acini with a diameter of 4.1 mm at a voxel size of 1.48 microm.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Anatomy, University of Bern, Switzerland. haberthuer@ana.unibe.ch

ABSTRACT
Volumetric data at micrometer level resolution can be acquired within a few minutes using synchrotron-radiation-based tomographic microscopy. The field of view along the rotation axis of the sample can easily be increased by stacking several tomograms, allowing the investigation of long and thin objects at high resolution. On the contrary, an extension of the field of view in the perpendicular direction is non-trivial. This paper presents an acquisition protocol which increases the field of view of the tomographic dataset perpendicular to its rotation axis. The acquisition protocol can be tuned as a function of the reconstruction quality and scanning time. Since the scanning time is proportional to the radiation dose imparted to the sample, this method can be used to increase the field of view of tomographic microscopy instruments while optimizing the radiation dose for radiation-sensitive samples and keeping the quality of the tomographic dataset on the required level. This approach, dubbed wide-field synchrotron radiation tomographic microscopy, can increase the lateral field of view up to five times. The method has been successfully applied for the three-dimensional imaging of entire rat lung acini with a diameter of 4.1 mm at a voxel size of 1.48 microm.

Show MeSH