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

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Vallejo Ramirez, Pedro P  ORCID logo
Zammit, Joseph 
Vanderpoorten, Oliver 
Riche, Fergus 
Blé, Francois-Xavier  ORCID logo


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.



5105 Medical and Biological Physics, 46 Information and Computing Sciences, 51 Physical Sciences, Bioengineering, Networking and Information Technology R&D (NITRD), Biomedical Imaging, Lung

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Springer Science and Business Media LLC


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Engineering and Physical Sciences Research Council (EP/L015889/1)
Wellcome Trust (203249/Z/16/Z)
Medical Research Council (MR/K015850/1)
Engineering and Physical Sciences Research Council (EP/H018301/1)
Wellcome Trust (089703/Z/09/Z)
Medical Research Council (MR/K02292X/1)