1. Steerable3D: An ImageJ plugin for neurovascular enhancement in 3-D segmentation
- Author
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Olli Gröhn, Alejandra Sierra, Marta Moraschi, Paolo Miocchi, Charles Nicaise, Alessia Cedola, Laura Maugeri, Francesco Brun, Alberto Mittone, Fabio Mangini, Michela Fratini, Lorenzo Massimi, Inna Bukreeva, Jussi Tohka, Federico Giove, Alberto Bravin, Eleonora Stefanutti, Ali Abdollahzadeh, Miocchi, P, Sierra, A, Maugeri, L, Stefanutti, E, Abdollahzadeh, A, Mangini, F, Moraschi, M, Bukreeva, I, Massimi, L, Brun, F, Tohka, J, Grohn, O, Mittone, A, Bravin, A, Nicaise, C, Giove, F, Cedola, A, Fratini, M, Miocchi, P., Sierra, A., Maugeri, L., Stefanutti, E., Abdollahzadeh, A., Mangini, F., Moraschi, M., Bukreeva, I., Massimi, L., Brun, F., Tohka, J., Grohn, O., Mittone, A., Bravin, A., Nicaise, C., Giove, F., Cedola, A., and Fratini, M.
- Subjects
Computer science ,Gaussian ,Biophysics ,General Physics and Astronomy ,Image processing ,030218 nuclear medicine & medical imaging ,03 medical and health sciences ,symbols.namesake ,0302 clinical medicine ,Imaging, Three-Dimensional ,Contrast-to-noise ratio ,Steerable filter ,Image noise ,Image Processing, Computer-Assisted ,X ray phase contrast tomography ,Radiology, Nuclear Medicine and imaging ,Segmentation ,Orientation (computer vision) ,business.industry ,Pattern recognition ,General Medicine ,Filter (signal processing) ,3D steerable filter ,Vascular network ,030220 oncology & carcinogenesis ,symbols ,Artificial intelligence ,business ,Algorithms - Abstract
Purpose Image processing plays a fundamental role in the study of central nervous system, for example in the analysis of the vascular network in neurodegenerative diseases. Synchrotron X-ray Phase-contrast micro-Tomography (SXPCT) is a very attractive method to study weakly absorbing samples and features, such as the vascular network in the spinal cord (SC). However, the identification and segmentation of vascular structures in SXPCT images is seriously hampered by the presence of image noise and strong contrast inhomogeneities, due to the sensitivity of the technique to small electronic density variations. In order to help with these tasks, we implemented a user-friendly ImageJ plugin based on a 3D Gaussian steerable filter, tuned up for the enhancement of tubular structures in SXPCT images. Methods The developed 3D Gaussian steerable filter plugin for ImageJ is based on the steerability properties of Gaussian derivatives. We applied it to SXPCT images of ex-vivo mouse SCs acquired at different experimental conditions. Results The filter response shows a strong amplification of the source image contrast-to-background ratio (CBR), independently of structures orientation. We found that after the filter application, the CBR ratio increases by a factor ranging from ~6 to ~60. In addition, we also observed an increase of 35% of the contrast to noise ratio in the case of injured mouse SC. Conclusion The developed tool can generally facilitate the detection/segmentation of capillaries, veins and arteries that were not clearly observable in non-filtered SXPCT images. Its systematic application could allow obtaining quantitative information from pre-clinical and clinical images.
- Published
- 2021