Mr-Nom: Multi-Scale Resolution of Neuronal Cells in Nissl-Stained Histological Slices Via Deliberate over-Segmentation and Merging

Conference paper

Vadori, V., Graïc, J-M., Finos, L., Corain, L., Peruffo, A. and Grisan, E. (2023). Mr-Nom: Multi-Scale Resolution of Neuronal Cells in Nissl-Stained Histological Slices Via Deliberate over-Segmentation and Merging. 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI). Cartegena de Indias, Colombia 18 - 21 Apr 2023 IEEE. https://doi.org/10.1109/isbi53787.2023.10230352
AuthorsVadori, V., Graïc, J-M., Finos, L., Corain, L., Peruffo, A. and Grisan, E.
TypeConference paper
Abstract

In comparative neuroanatomy, the characterization of brain cytoarchitecture is critical to a better understanding of brain structure and function, as it helps to distill information on the development, evolution, and distinctive features of different populations. The automatic segmentation of individual brain cells is a primary prerequisite and yet remains challenging. A new method (MR-NOM) was developed for the instance segmentation of cells in Nissl-stained histological images of the brain. MR-NOM exploits a multi-scale approach to deliberately over-segment the cells into superpixels and subsequently merge them via a classifier based on shape, structure, and intensity features. The method was tested on images of the cerebral cortex, proving successful in dealing with cells of varying characteristics that partially touch or overlap, showing better performance than two state-of-the-art methods.

Year2023
Journal2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI)
PublisherIEEE
ISSN1945-8452
Digital Object Identifier (DOI)https://doi.org/10.1109/isbi53787.2023.10230352
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Print18 Apr 2023
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Deposited16 Nov 2023
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Savioli, N., Visentin, S., Cosmi, E., Grisan, E., Lamata, P. and Montana, G. (2018). Temporal Convolution Networks for Real-Time Abdominal Fetal Aorta Analysis with Ultrasound. Artificial Neural Networks and Machine Learning – ICANN 2018. Rhodes, Greece 04 - 07 Oct 2018 Springer. https://doi.org/10.1007/978-3-030-01421-6_15
Quantitative imaging by pixel-based contrast-enhanced ultrasound reveals a linear relationship between synovial vascular perfusion and the recruitment of pathogenic IL-17A-F+IL-23+ CD161+ CD4+ T helper cells in psoriatic arthritis joints
Fiocco, U, Stramare, R, Martini, V, Coran, A, Caso, F, Costa, L, Felicetti, M, Rizzo, G, Tonietto, M, Scanu, A, Oliviero, F, Raffeiner, B, Vezzù, M, Lunardi, F, Scarpa, R, Sacerdoti, D, Rubaltelli, L, Punzi, L, Doria, A and Grisan, E (2017). Quantitative imaging by pixel-based contrast-enhanced ultrasound reveals a linear relationship between synovial vascular perfusion and the recruitment of pathogenic IL-17A-F+IL-23+ CD161+ CD4+ T helper cells in psoriatic arthritis joints. Clinical Rheumatology. 36 (2), pp. 391-399. https://doi.org/10.1007/s10067-016-3500-x
Boosting the Battery Life of Wearables for Health Monitoring Through the Compression of Biosignals
Hooshmand, M, Zordan, D, Del Testa, D, Grisan, E and Rossi, M (2017). Boosting the Battery Life of Wearables for Health Monitoring Through the Compression of Biosignals. IEEE Internet of Things Journal. 4, pp. 1647-1662. https://doi.org/10.1109/JIOT.2017.2689164
Detection of a slow-flow component in contrast-enhanced ultrasound of the synovia for the differential diagnosis of arthritis
Rizzo, G, Tonietto, M, Castellaro, M, Raffeiner, B, Coran, A, Fiocco, U, Stramare, R and Grisan, E (2017). Detection of a slow-flow component in contrast-enhanced ultrasound of the synovia for the differential diagnosis of arthritis. SPIE Medical Imaging. Orlando, FL, USA 11 - 16 Feb 2017 SPIE. https://doi.org/10.1117/12.2250818
Improving the quantification of contrast enhanced ultrasound using a Bayesian approach
Rizzo, G, Tonietto, M, Castellaro, M, Raffeiner, B, Coran, A, Fiocco, U, Stramare, R and Grisan, E (2017). Improving the quantification of contrast enhanced ultrasound using a Bayesian approach. SPIE Medical Imaging. Orlando, FL , USA 16 2016 - 11 Feb 2017 SPIE. https://doi.org/10.1117/12.2250195
Superpixel-based classification of gastric chromoendoscopy images
Boschetto, D and Grisan, E (2017). Superpixel-based classification of gastric chromoendoscopy images. SPIE Medical Imaging. Orlando, FL, USA 11 - 16 Feb 2017 SPIE. https://doi.org/10.1117/12.2254187
Boosted learned kernels for data-driven vesselness measure
Grisan, E (2017). Boosted learned kernels for data-driven vesselness measure. Proceedings Volume 10137, Medical Imaging 2017: Biomedical Applications in Molecular, Structural, and Functional Imaging; 101370Z (2017). Orlando, FL, USA 11 - 16 Feb 2017 SPIE. https://doi.org/10.1117/12.2250370
Cortical Thickness variability in Multiple Sclerosis: The role of lesion segmentation and filling
Palombit, A, Castellaro, M, Calabrese, M, Romualdi, C, Pizzini, FB, Montemezzi, S, Grisan, E and Bertoldo, A (2017). Cortical Thickness variability in Multiple Sclerosis: The role of lesion segmentation and filling. 2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017). Melbourne, VIC, Australia 18 - 21 Apr 2017 pp. 792-795 https://doi.org/10.1109/ISBI.2017.7950637
From macro to nano: Linking quantitative CEUS perfusion parameters to CD4+ T cells subtypes in spondyloarthtitis
Grisan, E, Rizzo, G, Tonietto, M, Coran, A, Raffeiner, B, Scanu, A, Martini, V, Stramare, R and Fiocco, U (2017). From macro to nano: Linking quantitative CEUS perfusion parameters to CD4+ T cells subtypes in spondyloarthtitis. 2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017). Melbourne, VIC, Australia 17 - 21 Apr 2017 Institute of Electrical and Electronics Engineers (IEEE). pp. 899-902 https://doi.org/10.1109/ISBI.2017.7950661
Grade and location of power doppler are predictive of damage progression in rheumatoid arthritis patients in clinical remission by anti-tumour necrosis factor α
Raffeiner, B, Grisan, E, Botsios, C, Stramare, R, Rizzo, G, Bernardi, L, Punzi, L, Ometto, F and Doria, A (2017). Grade and location of power doppler are predictive of damage progression in rheumatoid arthritis patients in clinical remission by anti-tumour necrosis factor α. Rheumatology (United Kingdom). 56, pp. 1320-1325. https://doi.org/10.1093/rheumatology/kex084
Bayesian Quantification of Contrast-Enhanced Ultrasound Images with Adaptive Inclusion of an Irreversible Component
Rizzo, G, Tonietto, M, Castellaro, M, Raffeiner, B, Coran, A, Fiocco, U, Stramare, R and Grisan, E (2017). Bayesian Quantification of Contrast-Enhanced Ultrasound Images with Adaptive Inclusion of an Irreversible Component. IEEE Transactions on Medical Imaging. 36, pp. 1027-1036. https://doi.org/10.1109/TMI.2016.2637698
Tcf7l2 plays pleiotropic roles in the control of glucose homeostasis, pancreas morphology, vascularization and regeneration
Facchinello, N, Tarifeño-Saldivia, E, Grisan, E, Schiavone, M, Peron, M, Mongera, A, Ek, O, Schmitner, N, Meyer, D, Peers, B, Tiso, N and Argenton, F (2017). Tcf7l2 plays pleiotropic roles in the control of glucose homeostasis, pancreas morphology, vascularization and regeneration. Scientific Reports. 7. https://doi.org/10.1038/s41598-017-09867-x
Growth abnormalities of fetuses and infants
Cosmi, E, Grisan, E, Fanos, V, Rizzo, G, Sivanandam, S and Visentin, S (2017). Growth abnormalities of fetuses and infants. BioMed Research International. 2017. https://doi.org/https://www.doi.org/10.1155/2017/3191308
A possible new approach in the prediction of late gestational hypertension: The role of the fetal aortic intima-media thickness
Visentin, S, Londero, AP, Camerin, M, Grisan, E and Cosmi, E (2017). A possible new approach in the prediction of late gestational hypertension: The role of the fetal aortic intima-media thickness. Medicine (United States). 96. https://doi.org/https://www.doi.org/10.1097/MD.0000000000005515
Automatic classification of small bowel mucosa alterations in celiac disease for confocal laser endomicroscopy
Boschetto, D, Di Claudio, G, Mirzaei, H, Leong, R and Grisan, E (2016). Automatic classification of small bowel mucosa alterations in celiac disease for confocal laser endomicroscopy. Medical Imaging 2016: Biomedical Applications in Molecular, Structural, and Functional Imaging. San Diego, United States 27 Feb - 03 Mar 2016 SPIE. https://doi.org/10.1117/12.2217183
Automatic classification of endoscopic images for premalignant conditions of the esophagus
Boschetto, D, Gambaretto, G and Grisan, E (2016). Automatic classification of endoscopic images for premalignant conditions of the esophagus. Medical Imaging 2016: Biomedical Applications in Molecular, Structural, and Functional Imaging. San Diego, United States 27 Feb - 03 Mar 2016 https://doi.org/10.1117/12.2216826
Superpixel-based automatic segmentation of villi in confocal endomicroscopy
Boschetto, D, Mirzaei, H, Leong, RWL and Grisan, E (2016). Superpixel-based automatic segmentation of villi in confocal endomicroscopy. 2016 IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI). Las Vegas, NV, USA 24 - 27 Feb 2016 pp. 168-171 https://doi.org/10.1109/BHI.2016.7455861
Quantification of kidneys from 3D ultrasound in pediatric hydronephrosis
Cerrolaza, J.J., Grisan, E., Safdar, N., Myers, E., Jago, J., Peters, C.A. and Linguraru, M.G. (2015). Quantification of kidneys from 3D ultrasound in pediatric hydronephrosis. Institute of Electrical and Electronics Engineers (IEEE). https://doi.org/10.1109/embc.2015.7318324