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

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

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

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

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

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

Influence of environmental factors on seed germination and seedling emergence of yellow sweet clover (Melilotus officinalis) Influência de fatores ambientais na germinação e emergência das plântulas de trevo doce amarelo (Melilotus officinalis)

Laboratory and greenhouse experiments were conducted to determine the effects of drought and salinity stress, temperature, pH and planting depth on yellow sweet clover (Melilotus officinalis) germination and emergence. Base, optimum and ceiling germination temperatures were estimated as 0, 18.47 and 34.60 ºC, respectively. Seed germination was sensitive to drought stress and completely inhibited at a potential of -1 MPa, but it was tolerant to salinity. Salinity stress up to 90 mM had no effect over the M. officinalis seed germination, but the germination decreased by increasing the salt concentration. The drought and salinity required for 50% inhibition of maximum germination were 207 mM and -0.49 MPa, respectively. High percentage of seed germination (>92%) was observed at pH = 5-6 and decreased to 80% at acidic medium (pH 4) and to 42% at alkaline medium (pH 9) pH. Maximum seedling emergence occurred when the seeds were placed at 2 cm depth and decreased when increasing the depth of planting; no seed emerged from depths of 10 cm.<br>Experimentos de laboratório e de casa-de-vegetação foram conduzidos para determinar os efeitos dos estresses de seca, salinidade, temperatura, pH e a profundidade de plantio sobre a germinação e a emergência do trevo amarelo doce (Melilotus officinalis). Temperaturas base, ótima e teto para germinação de M. officinalis foram estimados em 0, 18 e 34 ºC, respectivamente. A germinação das sementes mostrou-se sensível ao estresse hídrico e foi totalmente inibida nos potenciais de -1 MPa. A germinação de M. officinalis foi tolerante à salinidade. Estresse salino até 90 mM não tiveram efeito sobre a germinação de sementes de M. officinalis, mas a germinação decresceu com o aumento da concentração de sal. A seca e a salinidade necessária para inibição de 50% de germinação máxima foi de 207 mm e -0,49 MPa, respectivamente. Alta porcentagem de germinação (>92%) foi observada em pH = 5-6 e desceu para 80% em condições ácidas (pH 4) e para 42% sob condições alcalinas (pH 9). Emergência máxima ocorreu quando as sementes foram posicionadas na profundidade de 2 cm e diminuiu com o aumento da profundidade de plantio. Nenhuma semente emergiu quando a profundidade de semeadura foi de 10 cm

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

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

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

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