Deep learning-based instance segmentation for the precise automated quantification of digital breast cancer immunohistochemistry images

2022 ◽  
pp. 116471
Author(s):  
Blanca Maria Priego-Torres ◽  
Barbara Lobato-Delgado ◽  
Lidia Atienza-Cuevas ◽  
Daniel Sanchez-Morillo
Author(s):  
Ahmet Haşim Yurttakal ◽  
Hasan Erbay ◽  
Türkan İkizceli ◽  
Seyhan Karaçavuş ◽  
Cenker Biçer

Breast cancer is the most common cancer that progresses from cells in the breast tissue among women. Early-stage detection could reduce death rates significantly, and the detection-stage determines the treatment process. Mammography is utilized to discover breast cancer at an early stage prior to any physical sign. However, mammography might return false-negative, in which case, if it is suspected that lesions might have cancer of chance greater than two percent, a biopsy is recommended. About 30 percent of biopsies result in malignancy that means the rate of unnecessary biopsies is high. So to reduce unnecessary biopsies, recently, due to its excellent capability in soft tissue imaging, Dynamic Contrast-Enhanced Magnetic Resonance Imaging (DCE-MRI) has been utilized to detect breast cancer. Nowadays, DCE-MRI is a highly recommended method not only to identify breast cancer but also to monitor its development, and to interpret tumorous regions. However, in addition to being a time-consuming process, the accuracy depends on radiologists’ experience. Radiomic data, on the other hand, are used in medical imaging and have the potential to extract disease characteristics that can not be seen by the naked eye. Radiomics are hard-coded features and provide crucial information about the disease where it is imaged. Conversely, deep learning methods like convolutional neural networks(CNNs) learn features automatically from the dataset. Especially in medical imaging, CNNs’ performance is better than compared to hard-coded features-based methods. However, combining the power of these two types of features increases accuracy significantly, which is especially critical in medicine. Herein, a stacked ensemble of gradient boosting and deep learning models were developed to classify breast tumors using DCE-MRI images. The model makes use of radiomics acquired from pixel information in breast DCE-MRI images. Prior to train the model, radiomics had been applied to the factor analysis to refine the feature set and eliminate unuseful features. The performance metrics, as well as the comparisons to some well-known machine learning methods, state the ensemble model outperforms its counterparts. The ensembled model’s accuracy is 94.87% and its AUC value is 0.9728. The recall and precision are 1.0 and 0.9130, respectively, whereas F1-score is 0.9545.


Diagnostics ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 967
Author(s):  
Amirreza Mahbod ◽  
Gerald Schaefer ◽  
Christine Löw ◽  
Georg Dorffner ◽  
Rupert Ecker ◽  
...  

Nuclei instance segmentation can be considered as a key point in the computer-mediated analysis of histological fluorescence-stained (FS) images. Many computer-assisted approaches have been proposed for this task, and among them, supervised deep learning (DL) methods deliver the best performances. An important criterion that can affect the DL-based nuclei instance segmentation performance of FS images is the utilised image bit depth, but to our knowledge, no study has been conducted so far to investigate this impact. In this work, we released a fully annotated FS histological image dataset of nuclei at different image magnifications and from five different mouse organs. Moreover, by different pre-processing techniques and using one of the state-of-the-art DL-based methods, we investigated the impact of image bit depth (i.e., eight bits vs. sixteen bits) on the nuclei instance segmentation performance. The results obtained from our dataset and another publicly available dataset showed very competitive nuclei instance segmentation performances for the models trained with 8 bit and 16 bit images. This suggested that processing 8 bit images is sufficient for nuclei instance segmentation of FS images in most cases. The dataset including the raw image patches, as well as the corresponding segmentation masks is publicly available in the published GitHub repository.


Cancers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2764
Author(s):  
Xin Yu Liew ◽  
Nazia Hameed ◽  
Jeremie Clos

A computer-aided diagnosis (CAD) expert system is a powerful tool to efficiently assist a pathologist in achieving an early diagnosis of breast cancer. This process identifies the presence of cancer in breast tissue samples and the distinct type of cancer stages. In a standard CAD system, the main process involves image pre-processing, segmentation, feature extraction, feature selection, classification, and performance evaluation. In this review paper, we reviewed the existing state-of-the-art machine learning approaches applied at each stage involving conventional methods and deep learning methods, the comparisons within methods, and we provide technical details with advantages and disadvantages. The aims are to investigate the impact of CAD systems using histopathology images, investigate deep learning methods that outperform conventional methods, and provide a summary for future researchers to analyse and improve the existing techniques used. Lastly, we will discuss the research gaps of existing machine learning approaches for implementation and propose future direction guidelines for upcoming researchers.


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