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| Main Authors: | , , , , |
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| Format: | Preprint |
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2023
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| Subjects: | |
| Online Access: | https://arxiv.org/abs/2309.00911 |
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| _version_ | 1866910587658698752 |
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| author | Mamalakis, Michail Macfarlane, Sarah C. Notley, Scott V. Gad, Annica K. B Panoutsos, George |
| author_facet | Mamalakis, Michail Macfarlane, Sarah C. Notley, Scott V. Gad, Annica K. B Panoutsos, George |
| contents | We developed a transparent computational large-scale imaging-based framework that can distinguish between normal and metastasizing human cells. The method relies on fluorescence microscopy images showing the spatial organization of actin and vimentin filaments in normal and metastasizing single cells, using a combination of multi-attention channels network and global explainable techniques. We test a classification between normal cells (Bj primary fibroblast), and their isogenically matched, transformed and invasive counterpart (BjTertSV40TRasV12). Manual annotation is not trivial to automate due to the intricacy of the biologically relevant features. In this research, we utilized established deep learning networks and our new multi-attention channel architecture. To increase the interpretability of the network - crucial for this application area - we developed an interpretable global explainable approach correlating the weighted geometric mean of the total cell images and their local GradCam scores. The significant results from our analysis unprecedently allowed a more detailed, and biologically relevant understanding of the cytoskeletal changes that accompany oncogenic transformation of normal to invasive and metastasizing cells. We also paved the way for a possible spatial micrometre-level biomarker for future development of diagnostic tools against metastasis (spatial distribution of vimentin). |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2309_00911 |
| institution | arXiv |
| publishDate | 2023 |
| record_format | arxiv |
| spellingShingle | A novel framework employing deep multi-attention channels network for the autonomous detection of metastasizing cells through fluorescence microscopy Mamalakis, Michail Macfarlane, Sarah C. Notley, Scott V. Gad, Annica K. B Panoutsos, George Image and Video Processing Computer Vision and Pattern Recognition Machine Learning We developed a transparent computational large-scale imaging-based framework that can distinguish between normal and metastasizing human cells. The method relies on fluorescence microscopy images showing the spatial organization of actin and vimentin filaments in normal and metastasizing single cells, using a combination of multi-attention channels network and global explainable techniques. We test a classification between normal cells (Bj primary fibroblast), and their isogenically matched, transformed and invasive counterpart (BjTertSV40TRasV12). Manual annotation is not trivial to automate due to the intricacy of the biologically relevant features. In this research, we utilized established deep learning networks and our new multi-attention channel architecture. To increase the interpretability of the network - crucial for this application area - we developed an interpretable global explainable approach correlating the weighted geometric mean of the total cell images and their local GradCam scores. The significant results from our analysis unprecedently allowed a more detailed, and biologically relevant understanding of the cytoskeletal changes that accompany oncogenic transformation of normal to invasive and metastasizing cells. We also paved the way for a possible spatial micrometre-level biomarker for future development of diagnostic tools against metastasis (spatial distribution of vimentin). |
| title | A novel framework employing deep multi-attention channels network for the autonomous detection of metastasizing cells through fluorescence microscopy |
| topic | Image and Video Processing Computer Vision and Pattern Recognition Machine Learning |
| url | https://arxiv.org/abs/2309.00911 |