1. OptiJ: Open-source optical projection tomography of large organ samples
- Author
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Pelumi W. Oluwasanya, Romain F. Laine, Marcus Fantham, Dimitrios Simatos, Simeon E. Spasov, Omid Siddiqui, Xiao-Hong Zhou, Andrew Stretton, Oliver Hadeler, Clemens F. Kaminski, Eric J. Rees, Gemma Goodfellow, Bogdan F. Spiridon, Florian Ströhl, Oliver Vanderpoorten, Joseph Zammit, François-Xavier Blé, Farah Alimagham, Fergus Riche, Christopher J. Valentine, Pedro P. Vallejo Ramirez, Miranda Robbins, Vallejo Ramirez, Pedro P [0000-0002-7879-6761], Blé, Francois-Xavier [0000-0001-8561-9977], Laine, Romain F [0000-0002-2151-4487], Kaminski, Clemens F [0000-0002-5194-0962], Apollo - University of Cambridge Repository, Vallejo Ramirez, Pedro P. [0000-0002-7879-6761], Laine, Romain F. [0000-0002-2151-4487], and Kaminski, Clemens F. [0000-0002-5194-0962]
- Subjects
0301 basic medicine ,Computer science ,ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION ,lcsh:Medicine ,Bioengineering ,Imaging techniques ,01 natural sciences ,Optical projection tomography ,5105 Medical and Biological Physics ,Article ,010309 optics ,Set (abstract data type) ,03 medical and health sciences ,0302 clinical medicine ,46 Information and Computing Sciences ,Computer graphics (images) ,0103 physical sciences ,Microscopy ,lcsh:Science ,Lung ,030304 developmental biology ,0303 health sciences ,Multidisciplinary ,639/766/930/2735 ,lcsh:R ,Sample (graphics) ,030104 developmental biology ,Networking and Information Technology R&D (NITRD) ,14/63 ,Biomedical Imaging ,lcsh:Q ,51 Physical Sciences ,Biological fluorescence ,030217 neurology & neurosurgery ,631/57/2267 - 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.
- Published
- 2019