Estudio de respuesta a radiaciones ionizantes en zebrafish (Danio rerio) : diseño de sistemas de irradiación, dosimetría e imágenes / Study of response to ionizing in zabrafish (Danio rerio): desing of irradiation, dosimetry and imaging systems

Lado, Gerardo M. (2022) Estudio de respuesta a radiaciones ionizantes en zebrafish (Danio rerio) : diseño de sistemas de irradiación, dosimetría e imágenes / Study of response to ionizing in zabrafish (Danio rerio): desing of irradiation, dosimetry and imaging systems. Master in Physical Sciences, Universidad Nacional de Cuyo, Instituto Balseiro.


Abstract in Spanish

En este trabajo se desarrolló un sistema automatizado para la adquisición de imágenes radiográficas de muestras biológicas con resolución microscópica, utilizando dispositivos de producción masiva, bajo costo y fácil automatización, tales como sensores CMOS, motores paso a paso y sistemas de control basados en Arduino y Raspberry- Pi. Luego de elegir los componentes, el sistema fue construido, calibrado y optimizado para su uso con una fuente de rayos X con ánodo de tungsteno y otra con ánodo de cobre. Se evaluaron distintos algoritmos de procesamiento (filtrado y stitching) para la reconstrucción de imágenes y se estudió la relación contraste-ruido mínima necesaria para realizar reconstrucciones adecuadas para análisis anatómicos. Se tomaron imágenes por atenuación de rayos X de peces Zebrafish (Danio rerio) adultos y se evaluó el uso de compuestos de europio, gadolinio y iodo como agentes de contraste. Además, se tomaron radiografías de otras muestras biológicas para estudiar la aplicabilidad del método a otras muestras de interés. Los experimentos realizados permitieron obtener imágenes con resoluciones comparables a los sistemas comerciales e identificar estructuras internas en los peces. Este trabajo constituye un punto de partida para el desarrollo de sistemas mas complejos como, por ejemplo, sistemas de micro-tomografías por atenuación de rayos X. También permitiría ampliar los estudios realizables con Zebrafish, en particular aquellos sobre los efectos de radiación ionizante y sobre absorción de contaminantes en los tejidos de los peces.

Abstract in English

In this work, an automated system for the acquisition of microscopic resolution radiographic images of biological samples was developed. Mass-produced, low-cost and easily automated devices were used, such as CMOS sensors, stepper motors and control systems based on Arduino and RaspberryPi. The system was calibrated and optimized for use with X-ray sources. Different processing algorithms (filtering and stitching) for image reconstruction were evaluated and the minimum contrast-to-noise ratio necessary to perform suitable reconstructions for anatomical analysis was studied. X-ray attenuation images of adult Zebrafish (Danio rerio) were taken and the use of europium, gadolinium and iodine compounds as contrast agents was evaluated. In addition, radiographs of other biological samples were taken to study the applicability of the method to other samples of interest. The experiments carried out allowed us to to obtain images with resolutions comparable to commercial systems and to identify internal structures in the fish. This work constitutes a starting point for the development of more complex systems such as X-ray attenuation micro-tomography systems. It would also bring the possibility to expand the studies that can be carried out with Zebrafish, particularly those on the effects of ionizing radiation and absorption of heavy metal contaminants in fish tissues.

Item Type:Thesis (Master in Physical Sciences)
Keywords:Radiography (micro); Radiografía (micro); Dosimetry; Dosimetría; Images; Imágenes; X-rays; Rayos-X; [ Zebrafish; Bio-imaging; Bio-imágenes; CMOS sensors; Sensores CMOS; Digital processing; Procesamiento digital]
References:[1] Alcalde Bessia, F., P´erez, M., Lipovetzky, J., Piunno, N. A., Mateos, H., Sidelnik, I., et al. X-ray micrographic imaging system based on cots cmos sensors. International Journal of Circuit Theory and Applications, 46 (10), 1848–1857, 2018. 2, 15, 24, 35 [2] Feitsma, H., Cuppen, E. Zebrafish as a cancer model. Molecular Cancer Research, 6 (5), 685–694, 2008. 4 [3] Choi, T.-Y., Choi, T.-I., Lee, Y.-R., Choe, S.-K., Kim, C.-H. Zebrafish as an animal model for biomedical research. Experimental & Molecular Medicine, 53 (3), 310– 317, 2021. 4 [4] Ablain, J., Zon, L. I. Of fish and men: using zebrafish to fight human diseases. Trends in cell biology, 23 (12), 584–586, 2013. 4 [5] Cartner, S., Eisen, J. S., Farmer, S. F., Guillemin, K. J., Kent, M. L., Sanders, G. E. The Zebrafish in Biomedical Research: Biology, Husbandry, Diseases, and Research Applications. Academic Press, 2019. 4 [6] White, R. M., Sessa, A., Burke, C., Bowman, T., LeBlanc, J., Ceol, C., et al. Transparent adult zebrafish as a tool for in vivo transplantation analysis. Cell stem cell, 2 (2), 183–189, 2008. 4 [7] Tavares, B., Lopes, S. S. The importance of zebrafish in biomedical research. Acta medica portuguesa, 26 (5), 583–592, 2013. 4 [8] Menke, A. L., Spitsbergen, J. M., Wolterbeek, A. P., Woutersen, R. A. Normal anatomy and histology of the adult zebrafish. Toxicologic pathology, 39 (5), 759– 775, 2011. 4, 93 [9] Copper, J. E., Budgeon, L. R., Foutz, C. A., van Rossum, D. B., Vanselow, D. J., Hubley, M. J., et al. Comparative analysis of fixation and embedding techniques for optimized histological preparation of zebrafish. Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology, 208, 38–46, 2018. 4 [10] Fisher, S., Jagadeeswaran, P., Halpern, M. E. Radiographic analysis of zebrafish skeletal defects. Developmental biology, 264 (1), 64–76, 2003. 4, 5, 93 [11] Bryson-Richardson, R. J., Berger, S., Schilling, T. F., Hall, T. E., Cole, N. J., Gibson, A. J., et al. Fishnet: an online database of zebrafish anatomy. BMC biology, 5 (1), 1–8, 2007. 5 [12] Weinhardt, V., Shkarin, R., Wernet, T., Wittbrodt, J., Baumbach, T., Loosli, F. Quantitative morphometric analysis of adult teleost fish by x-ray computed tomography. Scientific reports, 8 (1), 1–12, 2018. 5, 90, 93, 94 [13] Ding, Y., Vanselow, D. J., Yakovlev, M. A., Katz, S. R., Lin, A. Y., Clark, D. P., et al. Computational 3d histological phenotyping of whole zebrafish by x-ray histotomography. Elife, 8, e44898, 2019. 5, 6 [14] Tonelli, F., Bek, J. W., Besio, R., De Clercq, A., Leoni, L., Salmon, P., et al. Zebrafish: a resourceful vertebrate model to investigate skeletal disorders. Frontiers in Endocrinology, 11, 2020. 5, 6, 93 [15] Howell, J. D. Early clinical use of the x-ray. Transactions of the American Clinical and Climatological Association, 127, 341, 2016. 7 [16] Allen, H. X-rays and their applications. Nature, 127 (3201), 356–358, 1931. 7 [17] Smith, N. B., Webb, A. Introduction to medical imaging: physics, engineering and clinical applications. Cambridge university press, 2010. 7, 8, 10, 11, 14, 15, 27, 29 [18] Ritman, E. L. Current status of developments and applications of micro-ct. Annual review of biomedical engineering, 13, 531–552, 2011. 7 [19] MacDonald, C. An Introduction to X-Ray Physics, Optics, and Applications. Princeton University Press, 2017. 7 [20] Cesareo, R. X-ray physics: Interaction with matter, production, detection. La Rivista del Nuovo Cimento, 23 (7), 1–231, 2000. 8, 9, 11, 12 [21] Seifert, M., Kaeppler, S., Hauke, C., Horn, F., Pelzer, G., Rieger, J., et al. Optimisation of image reconstruction for phase-contrast x-ray talbot–lau imaging with regard to mechanical robustness. Physics in Medicine & Biology, 61 (17), 6441, 2016. 9 [22] Knoll Glenn, F. Radiation detection and measurement. General Properties of Radiation Detectors, p´ags. 95–103, 2000. 9, 10, 11, 16 [23] Hirayama, H. Lecture note on photon interactions and cross sections. KEK, High Energy Accelerator Research Organization, Oho, Tsukuba, Ibaraki, Japan, 2000. 10, 11, 12 [24] Cowen, A. R. Cardiovascular x-ray imaging: Physics, equipment, and techniques. En: Textbook of Catheter-Based Cardiovascular Interventions, p´ags. 147– 198. Springer, 2018. 13 [25] Rawson, S. D., Maksimcuka, J., Withers, P. J., Cartmell, S. H. X-ray computed tomography in life sciences. BMC biology, 18 (1), 1–15, 2020. 13, 14 [26] Endrizzi, M. X-ray phase-contrast imaging. Nuclear instruments and methods in physics research section A: Accelerators, spectrometers, detectors and associated equipment, 878, 88–98, 2018. 13 [27] Jung, H. Basic physical principles and clinical applications of computed tomography. Progress in Medical Physics, 32 (1), 1–17, 2021. 14, 15 [28] Sharma, S. K. X-ray spectroscopy. BoD–Books on Demand, 2012. 15 [29] K.K, H. P. Technical note: X-ray detectors, Consultado el 19-jun-2021. URL 15,16 [30] Ponpon, J. Semiconductor detectors for 2d x-ray imaging. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 551 (1), 15–26, 2005. 15, 16, 19 [31] Perez, M., Haro, M. S., Lipovetzky, J., Cicuttin, A., Crespo, M. L., Bessia, F. A., et al. Evaluation of a commercial off the shelf cmos image sensor for x-ray spectroscopy up to 24.9 kev. Radiation Physics and Chemistry, 177, 109062, 2020. 16, 23 [32] Haro, M. S., Bessia, F. A., P´erez, M., Blostein, J. J., Balmaceda, D. F., Berisso, M. G., et al. Soft x-rays spectroscopy with a commercial cmos image sensor at room temperature. Radiation Physics and Chemistry, 167, 108354, 2020. 16, 23, 35 [33] Sze, S. M., Li, Y., Ng, K. K. Physics of semiconductor devices. John wiley & sons, 2021. 16, 22 [34] Kim, H. J., Kim, H. K., Cho, G., Choi, J. Construction and characterization of an amorphous silicon flat-panel detector based on ion shower doping process. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 505 (1-2), 155–158, 2003. 17, 18 [35] Risti´c, G. S. The digital flat-panel x-ray detectors. En: Proceedings of the third conference on medical physics and biomedical engineering, Association for medical physics and biomedical engineering in cooperation with the European federation of organisations for medical physics, pags. 65–71. 2013. 18 [36] Ted Pella, Inc. Background Information on CCD and CMOS Technology, Consultado en marzo 2021. URL 18, 20 [37] Thompson, A. C., Vaughan, D., et al. X-ray data booklet, tomo 8. Lawrence Berkeley National Laboratory, University of California Berkeley, CA, 2001. 19 [38] Chumacero, E. M. Estudio de la viabilidad del uso de detectores MEDIPIX en Fısica Medica. Tesis Doctoral, Benemerita Universidad Autonoma de Puebla, 2014. 19 [39] Granja, C., Polansky, S., Vykydal, Z., Pospisil, S., Owens, A., Kozacek, Z., et al. The satram timepix spacecraft payload in open space on board the proba-v satellite for wide range radiation monitoring in leo orbit. Planetary and Space Science, 125, 114–129, 2016. 20 [40] Hoffman, A., Loose, M., Suntharalingam, V. Cmos detector technology. Experimental Astronomy, 19 (1), 111–134, 2005. 21 [41] Bigas, M., Cabruja, E., Forest, J., Salvi, J. Review of cmos image sensors. Microelectronics journal, 37 (5), 433–451, 2006. 21, 22, 27 [42] El Gamal, A., Eltoukhy, H. Cmos image sensors. IEEE Circuits and Devices Magazine, 21 (3), 6–20, 2005. 22 [43] Lane, D. W. X-ray imaging and spectroscopy using low cost cots cmos sensors. Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 284, 29–32, 2012. 23 [44] Smith, S. T., Bednarek, D. R., Wobschall, D. C., Jeong, M., Kim, H., Rudin, S. Evaluation of a cmos image detector for low-cost and power medical x-ray imaging applications. En: Medical Imaging 1999: Physics of Medical Imaging, tomo 3659, pags. 952–961. International Society for Optics and Photonics, 1999. 23 [45] Lipovetzky, J., Cicuttin, A., Crespo, M. L., Haro, M. S., Bessia, F. A., P´erez, M., et al. Multi-spectral x-ray transmission imaging using a bsi cmos image sensor. Radiation Physics and Chemistry, 167, 108244, 2020. 23, 24 [46] Solutions, K. I. S. Ccd image sensor noise sources. Application Note Rev, 2, 2005. 25 [47] Dussault, D., Hoess, P. Noise performance comparison of iccd with ccd and emccd cameras. En: Infrared Systems and Photoelectronic Technology, tomo 5563, p´ags. 195–204. International Society for Optics and Photonics, 2004. [48] Tian, H. Noise analysis in CMOS image sensors. Tesis Doctoral, Citeseer, 2000. 25 [49] Mohammadnejad, S., Roshani, S., Sarvi, M. N. Fixed pattern noise reduction method in ccd sensors for leo satellite applications. En: Proceedings of the 11th International Conference on Telecommunications, p´ags. 441–446. IEEE, 2011. 27 [50] Gonzalez, R. C., Woods, R. E., Masters, B. R. Digital image processing, 2009. 28 [51] Lashansky, S. N., Mansbach, S., Berger, M. J., Karasik, T., Bin-Nun, M. Edge response revisited. En: Infrared Imaging Systems: Design, Analysis, Modeling, and Testing XIX, tomo 6941, p´ag. 69410Z. International Society for Optics and Photonics, 2008. 28 [52] Weisstein, E. W. Full width at half maximum. mathworld–a wolfram web resource, 2017. 29 [53] Audi, A., Pierrot-Deseilligny, M., Meynard, C., Thom, C. Implementation of an imu aided image stacking algorithm in a digital camera for unmanned aerial vehicles. Sensors, 17 (7), 1646, 2017. 29, 30 [54] Widiastuti, I., Muna, N., Purnomo, F. E., Lutfi, F., Soelaksini, L. D. Automatic image stitching of agriculture areas based on unmanned aerial vehicle using surf. En: Proceeding of the 1st International Conference on Food and Agriculture. 2018. [55] Shao, R., Du, C., Chen, H., Li, J. Fast anchor point matching for emergency uav image stitching using position and pose information. Sensors, 20 (7), 2007, 2020. 29 [56] Kale, P., Singh, K. A technical analysis of image stitching algorithm. International Journal of Computer Science and Information Technologies, 6 (1), 284–288, 2015. 29 [57] Rosten, E., Drummond, T. Fusing points and lines for high performance tracking. En: Tenth IEEE International Conference on Computer Vision (ICCV’05) Volume 1, tomo 2, p´ags. 1508–1515. Ieee, 2005. 29, 31 [58] Rublee, E., Rabaud, V., Konolige, K., Bradski, G. Orb: An efficient alternative to sift or surf. En: 2011 International conference on computer vision, p´ags. 2564–2571. eee, 2011. 30 [59] Oyallon, E., Rabin, J. An analysis of the surf method. Image Processing On Line, 5, 176–218, 2015. 30 [60] Bradski, G. The OpenCV Library. Dr. Dobb’s Journal of Software Tools, 2000. 31 [61] Gava, C., Bleser, G. 2d projective transformations (homographies). En: Technische Universit¨at Kaiserslautern. 31 [62] Brown, M., Lowe, D. G. Automatic panoramic image stitching using invariant features. International Journal of Computer Vision, 74 (1), 59–73, 2007. 31, 32, 39 [63] Bolles, R. C., Quam, L., Fischler, M. A., Wolf, H. C. Automatic determination of image-to-database correspondences. En: Proceedings of the 6th international joint conference on Artificial intelligence-Volume 1, p´ags. 73–78. 1979. 31 [64] Burt, P. J., Adelson, E. H. A multiresolution spline with application to image mosaics. ACM Transactions on Graphics (TOG), 2 (4), 217–236, 1983. 32 [65] Pyar, W. K., Yuttana, K. Automatic stitching of medical images using featurebased approach. Advances in Science, Technology and Eng. Systems, 4 (2), 127– 133, 2019. 33 [66] Perez, M., Alcalde, F., Haro, M. S., Sidelnik, I., Blostein, J. J., Berisso, M. G., et al. Implementation of an ionizing radiation detector based on a fpga-controlled cots cmos image sensor. En: 2017 XVII Workshop on Information Processing and Control (RPIC), p´ags. 1–6. IEEE, 2017. 35 [67] Arducam. Arducam usb camera shields, Consultado el 31-En-2022. URL 35 [68] Arducam. Arducam usb camera shields, Consultado el 31-En-2022. URL 36 [69] Open Source Contribution. Marlin Firmware., Consultado el 15-Sept-2019. 36 [70] Arduino. Arduino Mega 2560 Documentation. Arduino. URL https://store. 37 [71] Adrian Bowyer, The RepRap Project. RAMPS 1.4 RepRap wiki. RepRap. URL 37 [72] Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., et al. Fiji: an open-source platform for biological-image analysis. Nature methods, 9 (7), 676–682, 2012. 39 [73] Pablo d’Angelo, B. v. A., Florian Achleitner. Hugin panorama photo stitcher, 2019. 39 [74] AGS Equipamientos S.A. IMAX 70 MANUAL DE INSTRUCCIONES. AGS Equipamientos S.A, 2013. 42, 78 [75] Micron. MT9M001 - 1/2-Inch Megapixel Digital Image Sensor Features. Micron Technology, Inc, 2004. 45, 54 [76] Perez, M., Martınez, E., Lipovetzky, J., Mar´ın, J., Haro, M. S., Bessia, F. A., et al. High spatial resolution neutron detection technique based on commercial off-the-shelf cmos image sensors covered with nagdf 4 nanoparticles. Journal of Instrumentation, 16 (08), P08008, 2021. 64 [77] Hoffmann, T., Kutter, C., Santamaria, J. Capacity of salvinia minima baker to tolerate and accumulate as and pb. Engineering in Life Sciences, 4 (1), 61–65, 2004. 85 [78] Olguın, E. J., Sanchez-Galv´an, G., P´erez-P´erez, T., Perez-Orozco, A. Surface adsorption, intracellular accumulation and compartmentalization of pb (ii) in batchoperated lagoons with salvinia minima as affected by environmental conditions, edta and nutrients. Journal of Industrial Microbiology and Biotechnology, 32 (11- 12), 577–586, 2005. 85 [79] Babaei, F., Hong, T. L. C., Yeung, K., Cheng, S. H., Lam, Y. W. Contrastenhanced x-ray micro-computed tomography as a versatile method for anatomical studies of adult zebrafish. Zebrafish, 13 (4), 310–316, 2016. 90, 94 [80] Eshar, D., Latney, L., Wyre, N. R. Diagnostic contrast radiography in fish. Lab animal, 38 (10), 323–324, 2009. 90 [81] Speck, U. X-ray contrast media: overview, use and pharmaceutical aspects. Springer Nature, 2018. 90 [82] Attix, F. H. Introduction to radiological physics and radiation dosimetry. John Wiley & Sons, 2008. 99
Divisions:Gerencia de Area Medicina Nuclear
ID Code:1067
Deposited By:Tamara Cárcamo
Deposited On:26 Apr 2022 14:56
Last Modified:26 Apr 2022 14:56

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