| 1. |
- Balkenhol, Maschenka C. A., et al.
(författare)
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Deep learning assisted mitotic counting for breast cancer
- 2019
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Ingår i: Laboratory Investigation. - : NATURE PUBLISHING GROUP. - 0023-6837 .- 1530-0307. ; 99:11, s. 1596-1606
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Tidskriftsartikel (refereegranskat)abstract
- As part of routine histological grading, for every invasive breast cancer the mitotic count is assessed by counting mitoses in the (visually selected) region with the highest proliferative activity. Because this procedure is prone to subjectivity, the present study compares visual mitotic counting with deep learning based automated mitotic counting and fully automated hotspot selection. Two cohorts were used in this study. Cohort A comprised 90 prospectively included tumors which were selected based on the mitotic frequency scores given during routine glass slide diagnostics. This pathologist additionally assessed the mitotic count in these tumors in whole slide images (WSI) within a preselected hotspot. A second observer performed the same procedures on this cohort. The preselected hotspot was generated by a convolutional neural network (CNN) trained to detect all mitotic figures in digitized hematoxylin and eosin (Hamp;E) sections. The second cohort comprised a multicenter, retrospective TNBC cohort (n = 298), of which the mitotic count was assessed by three independent observers on glass slides. The same CNN was applied on this cohort and the absolute number of mitotic figures in the hotspot was compared to the averaged mitotic count of the observers. Baseline interobserver agreement for glass slide assessment in cohort A was good (kappa 0.689; 95% CI 0.580-0.799). Using the CNN generated hotspot in WSI, the agreement score increased to 0.814 (95% CI 0.719-0.909). Automated counting by the CNN in comparison with observers counting in the predefined hotspot region yielded an average kappa of 0.724. We conclude that manual mitotic counting is not affected by assessment modality (glass slides, WSI) and that counting mitotic figures in WSI is feasible. Using a predefined hotspot area considerably improves reproducibility. Also, fully automated assessment of mitotic score appears to be feasible without introducing additional bias or variability.
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| 2. |
- Dooper, Stephan, et al.
(författare)
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Gigapixel end-to-end training using streaming and attention
- 2023
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Ingår i: Medical Image Analysis. - : ELSEVIER. - 1361-8415 .- 1361-8423. ; 88
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Tidskriftsartikel (refereegranskat)abstract
- Current hardware limitations make it impossible to train convolutional neural networks on gigapixel image inputs directly. Recent developments in weakly supervised learning, such as attention-gated multiple instance learning, have shown promising results, but often use multi-stage or patch-wise training strategies risking suboptimal feature extraction, which can negatively impact performance. In this paper, we propose to train a ResNet-34 encoder with an attention-gated classification head in an end-to-end fashion, which we call StreamingCLAM, using a streaming implementation of convolutional layers. This allows us to train end-to-end on 4-gigapixel microscopic images using only slide-level labels.We achieve a mean area under the receiver operating characteristic curve of 0.9757 for metastatic breast cancer detection (CAMELYON16), close to fully supervised approaches using pixel-level annotations. Our model can also detect MYC-gene translocation in histologic slides of diffuse large B-cell lymphoma, achieving a mean area under the ROC curve of 0.8259. Furthermore, we show that our model offers a degree of interpretability through the attention mechanism.
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| 3. |
- Kartasalo, Kimmo, et al.
(författare)
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Artificial Intelligence for Diagnosis and Gleason Grading of Prostate Cancer in Biopsies-Current Status and Next Steps
- 2021
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Ingår i: European Urology Focus. - : Elsevier. - 2405-4569. ; 7:4, s. 687-691
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Forskningsöversikt (refereegranskat)abstract
- Diagnosis and Gleason grading of prostate cancer in biopsies are critical for the clinical management of men with prostate cancer. Despite this, the high grading variability among pathologists leads to the potential for under-and overtreatment. Artificial intelligence (AI) systems have shown promise in assisting pathologists to perform Gleason grading, which could help address this problem. In this mini-review, we highlight studies reporting on the development of AI systems for cancer detection and Gleason grading, and discuss the progress needed for widespread clinical implementation, as well as anticipated future developments. Patient summary: This mini-review summarizes the evidence relating to the validation of artificial intelligence (AI)-assisted cancer detection and Gleason grading of prostate cancer in biopsies, and highlights the remaining steps required prior to its widespread clinical implementation. We found that, although there is strong evidence to show that AI is able to perform Gleason grading on par with experienced uropathologists, more work is needed to ensure the accuracy of results from AI systems in diverse settings across different patient populations, digitization platforms, and pathology laboratories.
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| 4. |
- Pinckaers, Hans, et al.
(författare)
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Detection of Prostate Cancer in Whole-Slide Images Through End-to-End Training With Image-Level Labels
- 2021
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Ingår i: IEEE Transactions on Medical Imaging. - : IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. - 0278-0062 .- 1558-254X. ; 40:7, s. 1817-1826
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Tidskriftsartikel (refereegranskat)abstract
- Prostate cancer is the most prevalent cancer among men in Western countries, with 1.1 million new diagnoses every year. The gold standard for the diagnosis of prostate cancer is a pathologists evaluation of prostate tissue. To potentially assist pathologists deep/learning/based cancer detection systems have been developed. Many of the state-of-the- art models are patch/based convolutional neural networks, as the use of entire scanned slides is hampered by memory limitations on accelerator cards. Patch-based systems typically require detailed, pixel-level annotations for effective training. However, such annotations are seldom readily available, in contrast to the clinical reports of pathologists, which contain slide-level labels. As such, developing algorithms which do not require manual pixel-wise annotations, but can learn using only the clinical report would be a significant advancement for the field. In this paper, we propose to use a streaming implementation of convolutional layers, to train a modern CNN (ResNet/34) with 21 million parameters end-to-end on 4712 prostate biopsies. Themethod enables the use of entire biopsy images at high-resolution directly by reducing the GPUmemory requirements by 2.4 TB. We show thatmodern CNNs, trained using our streaming approach, can extract meaningful features from high-resolution images without additional heuristics, reaching similar performance as state-of-the-art patch-based and multiple-instance learning methods. By circumventing the need for manual annotations, this approach can function as a blueprint for other tasks in histopathological diagnosis. The source code to reproduce the streaming models is available at https://github.com/DIAGNijmegen/ pathology-streaming-pipeline.
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| 5. |
- Pinckaers, Hans, et al.
(författare)
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Predicting biochemical recurrence of prostate cancer with artificial intelligence
- 2022
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Ingår i: Communications Medicine. - : Nature Portfolio. - 2730-664X. ; 2:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: The first sign of metastatic prostate cancer after radical prostatectomy is rising PSA levels in the blood, termed biochemical recurrence. The prediction of recurrence relies mainly on the morphological assessment of prostate cancer using the Gleason grading system. However, in this system, within-grade morphological patterns and subtle histopathological features are currently omitted, leaving a significant amount of prognostic potential unexplored.Methods: To discover additional prognostic information using artificial intelligence, we trained a deep learning system to predict biochemical recurrence from tissue in H&E-stained microarray cores directly. We developed a morphological biomarker using convolutional neural networks leveraging a nested case-control study of 685 patients and validated on an independent cohort of 204 patients. We use concept-based explainability methods to interpret the learned tissue patterns.Results: The biomarker provides a strong correlation with biochemical recurrence in two sets (n = 182 and n = 204) from separate institutions. Concept-based explanations provided tissue patterns interpretable by pathologists.Conclusions: These results show that the model finds predictive power in the tissue beyond the morphological ISUP grading.
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| 6. |
- Swiderska-Chadaj, Zaneta, et al.
(författare)
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Learning to detect lymphocytes in immunohistochemistry with deep learning
- 2019
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Ingår i: Medical Image Analysis. - : ELSEVIER. - 1361-8415 .- 1361-8423. ; 58
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Tidskriftsartikel (refereegranskat)abstract
- The immune system is of critical importance in the development of cancer. The evasion of destruction by the immune system is one of the emerging hallmarks of cancer. We have built a dataset of 171,166 manually annotated CD3(+) and CD8(+) cells, which we used to train deep learning algorithms for automatic detection of lymphocytes in histopathology images to better quantify immune response. Moreover, we investigate the effectiveness of four deep learning based methods when different subcompartments of the whole-slide image are considered: normal tissue areas, areas with immune cell clusters, and areas containing artifacts. We have compared the proposed methods in breast, colon and prostate cancer tissue slides collected from nine different medical centers. Finally, we report the results of an observer study on lymphocyte quantification, which involved four pathologists from different medical centers, and compare their performance with the automatic detection. The results give insights on the applicability of the proposed methods for clinical use. U-Net obtained the highest performance with an F1-score of 0.78 and the highest agreement with manual evaluation (kappa = 0.72), whereas the average pathologists agreement with reference standard was kappa = 0.64. The test set and the automatic evaluation procedure are publicly available at lyon19.grand-challenge.org. (C) 2019 Elsevier B.V. All rights reserved.
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