OptiJ: Open-source optical projection tomography of large organ samples

2019 ◽  
Author(s):  
Mariana De Niz
Keyword(s):  
Open Source ◽  
Optical Projection Tomography ◽  
Optical Projection

scholarly journals OptiJ: Open-source optical projection tomography of large organ samples

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Pedro P. Vallejo Ramirez ◽  
Joseph Zammit ◽  
Oliver Vanderpoorten ◽  
Fergus Riche ◽  
Francois-Xavier Blé ◽  
...  
Keyword(s):  
Open Source ◽  
Low Cost ◽  
Three Dimensional ◽  
Optical Projection Tomography ◽  
Optical Components ◽  
Adult Mice ◽  
Optical Projection ◽  
Set Up ◽  
Imagej Plugin ◽  
Lung Lobes

Abstract The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples.

scholarly journals OPTiM: Optical projection tomography integrated microscope using open-source hardware and software

PLoS ONE ◽  
2017 ◽  
Vol 12 (7) ◽  
pp. e0180309 ◽  
Author(s):  
Thomas Watson ◽  
Natalie Andrews ◽  
Samuel Davis ◽  
Laurence Bugeon ◽  
Margaret D. Dallman ◽  
...  
Keyword(s):  
Open Source ◽  
Optical Projection Tomography ◽  
Optical Projection ◽  
Open Source Hardware

scholarly journals zOPT: an open source optical projection tomography system and methods for rapid 3D zebrafish imaging

2020 ◽  
Vol 11 (8) ◽  
pp. 4290 ◽  
Author(s):  
Hanqing Zhang ◽  
Laura Waldmann ◽  
Remy Manuel ◽  
Henrik Boije ◽  
Tatjana Haitina ◽  
...  
Keyword(s):  
Open Source ◽  
Optical Projection Tomography ◽  
Tomography System ◽  
Optical Projection

scholarly journals Open-Source Optical Projection Tomography of Large Organ Samples

2018 ◽  
Vol 114 (3) ◽  
pp. 346a ◽  
Author(s):  
Pedro P. Vallejo Ramirez ◽  
Joseph Zammit ◽  
Bogdan Spiridon ◽  
Fergus Riche ◽  
Florian Stroehl ◽  
...  
Keyword(s):  
Open Source ◽  
Optical Projection Tomography ◽  
Optical Projection

scholarly journals OptiJ: Open-source optical projection tomography of large organ samples

2019 ◽  
Author(s):  
Pedro P. Vallejo Ramirez ◽  
Joseph Zammit ◽  
Oliver Vanderpoorten ◽  
Fergus Riche ◽  
François-Xavier Blé ◽  
...  
Keyword(s):  
Open Source ◽  
Low Cost ◽  
Three Dimensional ◽  
Optical Projection Tomography ◽  
Optical Components ◽  
Adult Mice ◽  
Optical Projection ◽  
Set Up ◽  
Imagej Plugin ◽  
Lung Lobes

The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 μm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples.

Time gated optical projection tomography for 3D imaging of highly scattering biological models

2010 ◽  
Author(s):  
Andrea Bassi ◽  
Daniele Brida ◽  
Cosimo D’Andrea ◽  
Gianluca Valentini ◽  
Sandro De Silvestri ◽  
...  
Keyword(s):  
3D Imaging ◽  
Optical Projection Tomography ◽  
Biological Models ◽  
Optical Projection

Optical Projection Tomography for Particle Counting and Morphology Analysis

2020 ◽  
pp. 944-951
Author(s):  
Olli Koskela ◽  
Md Tanvirul Kabir Chowdhury ◽  
Toni Montonen ◽  
Birhanu Belay ◽  
Sampsa Pursiainen ◽  
...  
Keyword(s):  
Optical Projection Tomography ◽  
Optical Projection ◽  
Particle Counting ◽  
Morphology Analysis
Sign in / Sign up

Export Citation Format

Share Document