1
|
Sheikh TS, Cho M. Segmentation of Variants of Nuclei on Whole Slide Images by Using Radiomic Features. Bioengineering (Basel) 2024; 11:252. [PMID: 38534526 DOI: 10.3390/bioengineering11030252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/10/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
The histopathological segmentation of nuclear types is a challenging task because nuclei exhibit distinct morphologies, textures, and staining characteristics. Accurate segmentation is critical because it affects the diagnostic workflow for patient assessment. In this study, a framework was proposed for segmenting various types of nuclei from different organs of the body. The proposed framework improved the segmentation performance for each nuclear type using radiomics. First, we used distinct radiomic features to extract and analyze quantitative information about each type of nucleus and subsequently trained various classifiers based on the best input sub-features of each radiomic feature selected by a LASSO operator. Second, we inputted the outputs of the best classifier to various segmentation models to learn the variants of nuclei. Using the MoNuSAC2020 dataset, we achieved state-of-the-art segmentation performance for each category of nuclei type despite the complexity, overlapping, and obscure regions. The generalized adaptability of the proposed framework was verified by the consistent performance obtained in whole slide images of different organs of the body and radiomic features.
Collapse
Affiliation(s)
- Taimoor Shakeel Sheikh
- AIMI-Artificial Intelligence and Medical Imaging Laboratory, Department of Computer & Media Engineering, Tongmyong University, Busan 48520, Republic of Korea
| | - Migyung Cho
- AIMI-Artificial Intelligence and Medical Imaging Laboratory, Department of Computer & Media Engineering, Tongmyong University, Busan 48520, Republic of Korea
| |
Collapse
|
2
|
Prencipe B, Delprete C, Garolla E, Corallo F, Gravina M, Natalicchio MI, Buongiorno D, Bevilacqua V, Altini N, Brunetti A. An Explainable Radiogenomic Framework to Predict Mutational Status of KRAS and EGFR in Lung Adenocarcinoma Patients. Bioengineering (Basel) 2023; 10:747. [PMID: 37508774 PMCID: PMC10376018 DOI: 10.3390/bioengineering10070747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/17/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
The complex pathobiology of lung cancer, and its spread worldwide, has prompted research studies that combine radiomic and genomic approaches. Indeed, the early identification of genetic alterations and driver mutations affecting the tumor is fundamental for correctly formulating the prognosis and therapeutic response. In this work, we propose a radiogenomic workflow to detect the presence of KRAS and EGFR mutations using radiomic features extracted from computed tomography images of patients affected by lung adenocarcinoma. To this aim, we investigated several feature selection algorithms to identify the most significant and uncorrelated sets of radiomic features and different classification models to reveal the mutational status. Then, we employed the SHAP (SHapley Additive exPlanations) technique to increase the understanding of the contribution given by specific radiomic features to the identification of the investigated mutations. Two cohorts of patients with lung adenocarcinoma were used for the study. The first one, obtained from the Cancer Imaging Archive (TCIA), consisted of 60 cases (25% EGFR, 23% KRAS); the second one, provided by the Azienda Ospedaliero-Universitaria 'Ospedali Riuniti' of Foggia, was composed of 55 cases (16% EGFR, 28% KRAS). The best-performing models proposed in our study achieved an AUC of 0.69 and 0.82 on the validation set for predicting the mutational status of EGFR and KRAS, respectively. The Multi-layer Perceptron model emerged as the top-performing model for both oncogenes, in some cases outperforming the state of the art. This study showed that radiomic features can be associated with EGFR and KRAS mutational status in patients with lung adenocarcinoma.
Collapse
Affiliation(s)
- Berardino Prencipe
- Department of Electrical and Information Engineering, Polytechnic University of Bari, Via Orabona 4, 70126 Bari, Italy
| | - Claudia Delprete
- Department of Electrical and Information Engineering, Polytechnic University of Bari, Via Orabona 4, 70126 Bari, Italy
| | - Emilio Garolla
- Department of Medical and Surgical Sciences, University of Foggia, Viale Pinto 1, 71122 Foggia, Italy
| | - Fabio Corallo
- Department of Medical and Surgical Sciences, University of Foggia, Viale Pinto 1, 71122 Foggia, Italy
| | - Matteo Gravina
- Department of Medical and Surgical Sciences, University of Foggia, Viale Pinto 1, 71122 Foggia, Italy
| | - Maria Iole Natalicchio
- Molecular Oncology and Pharmacogenomics Laboratory, University of Foggia, Viale Pinto 1, 71122 Foggia, Italy
| | - Domenico Buongiorno
- Department of Electrical and Information Engineering, Polytechnic University of Bari, Via Orabona 4, 70126 Bari, Italy
- Apulian Bioengineering SRL, Via delle Violette 14, 70026 Modugno, Italy
| | - Vitoantonio Bevilacqua
- Department of Electrical and Information Engineering, Polytechnic University of Bari, Via Orabona 4, 70126 Bari, Italy
- Apulian Bioengineering SRL, Via delle Violette 14, 70026 Modugno, Italy
| | - Nicola Altini
- Department of Electrical and Information Engineering, Polytechnic University of Bari, Via Orabona 4, 70126 Bari, Italy
| | - Antonio Brunetti
- Department of Electrical and Information Engineering, Polytechnic University of Bari, Via Orabona 4, 70126 Bari, Italy
- Apulian Bioengineering SRL, Via delle Violette 14, 70026 Modugno, Italy
| |
Collapse
|
3
|
Altini N, Puro E, Taccogna MG, Marino F, De Summa S, Saponaro C, Mattioli E, Zito FA, Bevilacqua V. Tumor Cellularity Assessment of Breast Histopathological Slides via Instance Segmentation and Pathomic Features Explainability. Bioengineering (Basel) 2023; 10:396. [PMID: 37106583 PMCID: PMC10135772 DOI: 10.3390/bioengineering10040396] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/14/2023] [Accepted: 03/19/2023] [Indexed: 04/29/2023] Open
Abstract
The segmentation and classification of cell nuclei are pivotal steps in the pipelines for the analysis of bioimages. Deep learning (DL) approaches are leading the digital pathology field in the context of nuclei detection and classification. Nevertheless, the features that are exploited by DL models to make their predictions are difficult to interpret, hindering the deployment of such methods in clinical practice. On the other hand, pathomic features can be linked to an easier description of the characteristics exploited by the classifiers for making the final predictions. Thus, in this work, we developed an explainable computer-aided diagnosis (CAD) system that can be used to support pathologists in the evaluation of tumor cellularity in breast histopathological slides. In particular, we compared an end-to-end DL approach that exploits the Mask R-CNN instance segmentation architecture with a two steps pipeline, where the features are extracted while considering the morphological and textural characteristics of the cell nuclei. Classifiers that are based on support vector machines and artificial neural networks are trained on top of these features in order to discriminate between tumor and non-tumor nuclei. Afterwards, the SHAP (Shapley additive explanations) explainable artificial intelligence technique was employed to perform a feature importance analysis, which led to an understanding of the features processed by the machine learning models for making their decisions. An expert pathologist validated the employed feature set, corroborating the clinical usability of the model. Even though the models resulting from the two-stage pipeline are slightly less accurate than those of the end-to-end approach, the interpretability of their features is clearer and may help build trust for pathologists to adopt artificial intelligence-based CAD systems in their clinical workflow. To further show the validity of the proposed approach, it has been tested on an external validation dataset, which was collected from IRCCS Istituto Tumori "Giovanni Paolo II" and made publicly available to ease research concerning the quantification of tumor cellularity.
Collapse
Affiliation(s)
- Nicola Altini
- Department of Electrical and Information Engineering (DEI), Polytechnic University of Bari, Via Edoardo Orabona n. 4, 70126 Bari, Italy
| | - Emilia Puro
- Department of Electrical and Information Engineering (DEI), Polytechnic University of Bari, Via Edoardo Orabona n. 4, 70126 Bari, Italy
| | - Maria Giovanna Taccogna
- Department of Electrical and Information Engineering (DEI), Polytechnic University of Bari, Via Edoardo Orabona n. 4, 70126 Bari, Italy
| | - Francescomaria Marino
- Department of Electrical and Information Engineering (DEI), Polytechnic University of Bari, Via Edoardo Orabona n. 4, 70126 Bari, Italy
| | - Simona De Summa
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS Istituto Tumori “Giovanni Paolo II”, Via O. Flacco n. 65, 70124 Bari, Italy
| | - Concetta Saponaro
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Via Padre Pio n. 1, 85028 Rionero in Vulture, Italy
| | - Eliseo Mattioli
- Pathology Department, IRCCS Istituto Tumori “Giovanni Paolo II”, Via O. Flacco n. 65, 70124 Bari, Italy
| | - Francesco Alfredo Zito
- Pathology Department, IRCCS Istituto Tumori “Giovanni Paolo II”, Via O. Flacco n. 65, 70124 Bari, Italy
| | - Vitoantonio Bevilacqua
- Department of Electrical and Information Engineering (DEI), Polytechnic University of Bari, Via Edoardo Orabona n. 4, 70126 Bari, Italy
- Apulian Bioengineering s.r.l., Via delle Violette n. 14, 70026 Modugno, Italy
| |
Collapse
|
4
|
Bidzińska J, Szurowska E. See Lung Cancer with an AI. Cancers (Basel) 2023; 15:1321. [PMID: 36831662 PMCID: PMC9954317 DOI: 10.3390/cancers15041321] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
A lot has happened in the field of lung cancer screening in recent months. The ongoing discussion and documentation published by the scientific community and policymakers are of great importance to the entire European community and perhaps beyond. Lung cancer is the main worldwide killer. Low-dose computed tomography-based screening, together with smoking cessation, is the only tool to fight lung cancer, as it has already been proven in the United States of America but also European randomized controlled trials. Screening requires a lot of well-organized specialized work, but it can be supported by artificial intelligence (AI). Here we discuss whether and how to use AI for patients, radiologists, pulmonologists, thoracic surgeons, and all hospital staff supporting screening process benefits.
Collapse
Affiliation(s)
- Joanna Bidzińska
- Second Department of Radiology, Medical University of Gdansk, 80-210 Gdańsk, Poland
| | | |
Collapse
|
5
|
A Fusion Biopsy Framework for Prostate Cancer Based on Deformable Superellipses and nnU-Net. Bioengineering (Basel) 2022; 9:bioengineering9080343. [PMID: 35892756 PMCID: PMC9394419 DOI: 10.3390/bioengineering9080343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/13/2022] [Accepted: 07/21/2022] [Indexed: 11/24/2022] Open
Abstract
In prostate cancer, fusion biopsy, which couples magnetic resonance imaging (MRI) with transrectal ultrasound (TRUS), poses the basis for targeted biopsy by allowing the comparison of information coming from both imaging modalities at the same time. Compared with the standard clinical procedure, it provides a less invasive option for the patients and increases the likelihood of sampling cancerous tissue regions for the subsequent pathology analyses. As a prerequisite to image fusion, segmentation must be achieved from both MRI and TRUS domains. The automatic contour delineation of the prostate gland from TRUS images is a challenging task due to several factors including unclear boundaries, speckle noise, and the variety of prostate anatomical shapes. Automatic methodologies, such as those based on deep learning, require a huge quantity of training data to achieve satisfactory results. In this paper, the authors propose a novel optimization formulation to find the best superellipse, a deformable model that can accurately represent the prostate shape. The advantage of the proposed approach is that it does not require extensive annotations, and can be used independently of the specific transducer employed during prostate biopsies. Moreover, in order to show the clinical applicability of the method, this study also presents a module for the automatic segmentation of the prostate gland from MRI, exploiting the nnU-Net framework. Lastly, segmented contours from both imaging domains are fused with a customized registration algorithm in order to create a tool that can help the physician to perform a targeted prostate biopsy by interacting with the graphical user interface.
Collapse
|