Evaluation of scan strategies for small animal in-vivo ... › event › 774201 › contributions...

Evaluation of scan strategiesfor small animal in-vivo micro-CT

1

J. Zemlicka1, J. Dudak 1, P. Rubovic 1, J. Mrzilkova 2,

L. Judas 3, D. Ekendahl 3

1 Institute of Experimental and Applied Physics, Czech Technical University in Prague2 3rd Faculty of Medicine, Charles University in Prague3 National Radiation Protection Institute, v.v.i.

IWORID 2019, Kolympari, Greece - Jan Zemlicka, IEAP CTU in Prague8th July 2019

Outline

• Timepix based micro-CT scanners

• Post mortem high resolution imaging

• Towards in-vivo imaging – dose estimation

• Plastimouse phantom

• Scan strategies

• Available options for dose reduction

IWORID 2019, Kolympari, Greece - Jan Zemlicka, IEAP CTU in Prague 28th July 2019

Timepix based micro-CT scanners at IEAP• Several CT systems are operated in imaging laboratory

• Nano-focus and micro-focus X-ray tubes

• Sample size: 1–100 mm

• Voxel resolution resolution: 0.5-50 µm

• Equipped with Timepix large are detectors:

• Quad to Widepix10×5• 300 µm Si or 1000 µm CdTe sensors

• Threshold level above the electronics noise in each pixel -> no dark/leakage current

• Virtually unlimited dynamic range (long exposure time is possible)

• Poissonian distribution of detected photons-> SNR is given just by the number of the detected photons


Post mortem high resolution imaging

• Laboratory mouse

• Cone beam scan

• 720 projections

• 10.5 s acquisition time

• 0.5 degree step

• scan time 180 min (exposure time 126 min)

• EPS = 31.6 µm

• Standard contrast agentscan be used


1 cm

1 cm

Towards in-vivo imaging• Small animals in pre-clinical research (mouse, rat)

• Diameter < 50 mm of soft tissue, air bubbles and bones

• Commonly used X-ray spectrum

• 70 kVp and 150 µA

• filtered by 250 µm Aluminium


Dose measurement • cylindrical polyethylene phantom (20 mm

diameter)

• thermoluminescent dosimeters (MCP-7P,

TLD Poland)

• Average dose rate 2.1 mGy/s

• Imunosupression was reported after exposing

mice to 100-500 mGy

=> scan time should be ~ 50-250 seconds

Plastimouse phantom• Ethical choice for research

• Biologically inert

• Motionless rigid object

• Represents true anatomy of living mouse


angular range

angle step

Real measurement times

acquisition time

frame readout time

gantry movement


Exposure time:

• Acquisition time: 250 ms – 30 s

• Angular range: 195 or 360 degrees for cone beam scan

720 – 3600 degrees for spiral scan

• Angle step: 0.2 – 2 degrees

𝑡𝑖𝑚𝑒 = 𝑝𝑟𝑜𝑗𝑒𝑐𝑡𝑖𝑜𝑛 𝑡𝑖𝑚𝑒 × 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑝𝑟𝑜𝑗𝑒𝑐𝑡𝑖𝑜𝑛𝑠

×

Extra time:

- Readout speed of large area Timepix detector: > 200 ms

- Gantry movement: 600 - 1000 ms

Scanning strategiesIdealized case: scan time = acq. time × no. projections

• Angular sampling (number of projections)

0.5, 0.6, 1.0, 1.2, 1.5, 1.8, 2.0 degree

• Acquisiton time (statistics in each projection)

0.25, 0.50, 1.00, 1.50, 2.00, 3.00 s

• 195 and 360 degree rotations


2500 mGy 205 mGy 51 mGy

Average dose rate

2.1 mGy/s

300 µm 300 µm 300 µm

Angular step and acquisition time

• a


97.5 s

24.4 s

195 s

48.8 s

390 s

97.5 s

780 s

195 s

0.25 s 0.5 s 1 s 2sAcq. time

An

gula

r st

ep2

deg

.

0.5

deg

.

Fixed exposure time 97.5s


97.5 s

97.5 s

0.5 deg

390 proj.

0.25 s

2 deg

96 proj.

1 s

300 µm

300 µm

Fixed exposure time 97.5s


97.5 s 97.5 s

ang. step 0.5 deg - acq. time 0.25 s ang. step 2 deg - acq. time 1 s

Contrast-to-noise ratio

skin

muscle

bladder

bone

reference area


𝑪𝑵𝑹 =𝒎𝒆𝒂𝒏 𝒓𝒐𝒊 −𝒎𝒆𝒂𝒏(𝒓𝒆𝒇)

𝒔𝒕𝒅(𝒓𝒆𝒇)

Selected areas:

Fixed exposure time and angular range

Fixed exposure and acq. time

Bone structures


ang. step 0.5 deg - acq. time 3 s ang. step 2 deg - acq. time 0.25 s

CNR 48.62 CNR 8.38

Available options for dose reduction

Exposure time:

• Spectrum filtering → based on the sample type and size (mouse, rat)

• Alternative high Z sensor (GaAs, CdTe) → improved detection efficiency up to 99% for 70 kVp spectrum

Extra time:

• Faster detector readout → after each frame (multiplied for integral frames)

• Gantry speed → time between projections

• X-ray tube fast switch on/off

• Fast shutter → sample is irradiated only during acquisitions


Conclusions

• Dose limit is 100 – 500 mGy

• Average dose rate in our system is 2.1 mGy/s

• post mortem exposure time 60 minutes needs to be reduced to ~ 50-150 s

• Exposure time of 100 s and 0.5 degree angular sampling gives us CNR:

• soft tissues in a range of 2.25 – 4.65

• bones 20.33

• Improved detection efficiency of CdTe sensor can decrease exposure time by factor of 3

• Software and hardware adaptations leading to extra time reduction are needed for in-vivo measurements


IWORID 2019, Kolympari, Greece - Jan Zemlicka, IEAP CTU in Prague 16

Thank you for your attention.

Questions?

8th July 2019

500 µm

Evaluation of scan strategies for small animal in-vivo ... › event › 774201 › contributions...

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