Label-efficient Contrastive Learning-based model for nuclei detection and classification in 3D Cardiovascular Immunofluorescent Images
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| Format: | Preprint |
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2023
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| _version_ | 1866909072583819264 |
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| author | Moradinasab, Nazanin Deaton, Rebecca A. Shankman, Laura S. Owens, Gary K. Brown, Donald E. |
| author_facet | Moradinasab, Nazanin Deaton, Rebecca A. Shankman, Laura S. Owens, Gary K. Brown, Donald E. |
| contents | Recently, deep learning-based methods achieved promising performance in nuclei detection and classification applications. However, training deep learning-based methods requires a large amount of pixel-wise annotated data, which is time-consuming and labor-intensive, especially in 3D images. An alternative approach is to adapt weak-annotation methods, such as labeling each nucleus with a point, but this method does not extend from 2D histopathology images (for which it was originally developed) to 3D immunofluorescent images. The reason is that 3D images contain multiple channels (z-axis) for nuclei and different markers separately, which makes training using point annotations difficult. To address this challenge, we propose the Label-efficient Contrastive learning-based (LECL) model to detect and classify various types of nuclei in 3D immunofluorescent images. Previous methods use Maximum Intensity Projection (MIP) to convert immunofluorescent images with multiple slices to 2D images, which can cause signals from different z-stacks to falsely appear associated with each other. To overcome this, we devised an Extended Maximum Intensity Projection (EMIP) approach that addresses issues using MIP. Furthermore, we performed a Supervised Contrastive Learning (SCL) approach for weakly supervised settings. We conducted experiments on cardiovascular datasets and found that our proposed framework is effective and efficient in detecting and classifying various types of nuclei in 3D immunofluorescent images. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2309_03744 |
| institution | arXiv |
| publishDate | 2023 |
| record_format | arxiv |
| spellingShingle | Label-efficient Contrastive Learning-based model for nuclei detection and classification in 3D Cardiovascular Immunofluorescent Images Moradinasab, Nazanin Deaton, Rebecca A. Shankman, Laura S. Owens, Gary K. Brown, Donald E. Image and Video Processing Computer Vision and Pattern Recognition Recently, deep learning-based methods achieved promising performance in nuclei detection and classification applications. However, training deep learning-based methods requires a large amount of pixel-wise annotated data, which is time-consuming and labor-intensive, especially in 3D images. An alternative approach is to adapt weak-annotation methods, such as labeling each nucleus with a point, but this method does not extend from 2D histopathology images (for which it was originally developed) to 3D immunofluorescent images. The reason is that 3D images contain multiple channels (z-axis) for nuclei and different markers separately, which makes training using point annotations difficult. To address this challenge, we propose the Label-efficient Contrastive learning-based (LECL) model to detect and classify various types of nuclei in 3D immunofluorescent images. Previous methods use Maximum Intensity Projection (MIP) to convert immunofluorescent images with multiple slices to 2D images, which can cause signals from different z-stacks to falsely appear associated with each other. To overcome this, we devised an Extended Maximum Intensity Projection (EMIP) approach that addresses issues using MIP. Furthermore, we performed a Supervised Contrastive Learning (SCL) approach for weakly supervised settings. We conducted experiments on cardiovascular datasets and found that our proposed framework is effective and efficient in detecting and classifying various types of nuclei in 3D immunofluorescent images. |
| title | Label-efficient Contrastive Learning-based model for nuclei detection and classification in 3D Cardiovascular Immunofluorescent Images |
| topic | Image and Video Processing Computer Vision and Pattern Recognition |
| url | https://arxiv.org/abs/2309.03744 |