Nuclei & Glands Instance Segmentation in Histology Images: A Narrative Review

Instance segmentation of nuclei and glands in the histology images is an important step in computational pathology workflow for cancer diagnosis, treatment planning and survival analysis. With the advent of modern hardware, the recent availability of large-scale quality public datasets and the community organized grand challenges have seen a surge in automated methods focusing on domain specific challenges, which is pivotal for technology advancements and clinical translation. In this survey, 126 papers illustrating the AI based methods for nuclei and glands instance segmentation published in the last five years (2017-2022) are deeply analyzed, the limitations of current approaches and the open challenges are discussed. Moreover, the potential future research direction is presented and the contribution of state-of-the-art methods is summarized. Further, a generalized summary of publicly available datasets and a detailed insights on the grand challenges illustrating the top performing methods specific to each challenge is also provided. Besides, we intended to give the reader current state of existing research and pointers to the future directions in developing methods that can be used in clinical practice enabling improved diagnosis, grading, prognosis, and treatment planning of cancer. To the best of our knowledge, no previous work has reviewed the instance segmentation in histology images focusing towards this direction.Comment: 60 pages, 14 figure

Deteksi Wanita Berhijab dan tidak Berhijab dengan menggunakan Metode Mask RCNN

Setiap santriwati yang tinggal di pesantren wajib menggunakan hijab. Untuk melakukan control dan monitoring penggunaan hijab di pesantren saat ini masih dilakukan secara manual oleh pihak keamanan. Proses control dan monitoring yang dilakukan secara manual ini membutuhkan waktu dan proses yang lama serta membutuhkan sumber daya manusia yang banyak. Untuk membantu mengatasi permasalahan yang ada, maka dibutuhkan sistem yang dapat memonitoring pemakaian hijab secara otomatis. Pada penelitian ini diusulkan menggunakan metode MASK RCNN untuk mendeteksi objek wanita yang tidak berhijab dan wanita yang berhijab dari gambar digital. Dataset yang digunakan pada penelitian ini terdapat 3 kategori yaitu wanita berhijab syar’i, wanita berhijab tidak syar’i, dan wanita tidak berhijab yang memiliki 4 class yaitu wajah, rambut, hijab syar’i, hijab non syar’i. Proses yang dilakukan pada metode tersebut terdapat 2 tahapan yaitu data training dan data testing. Data training yang digunakan adalah 1500 citra digital setiap kategori berjumlah 500 citra digital dan data testing yaitu digunakan 150 gambar setiap kategori berjumlah 50 gambar. Model ini dilatih dengan metode MASK RCNN data training memperoleh epoch 30 dengan nilai loss 0,1770, nilai val_loss 0,1745 dan waktu 473s 946ms/step. Hasil eksperimen menunjukkan bahwa metode yang diusulkan dapat mendeteki hijab syar’i dengan tingkat akurasi 96%, hijab tidak syar’i dengan tingkat akurasi 96 % dan tidak berhijab dengan tingkat akurasi 94%

Fast Synthetic Dataset for Kitchen Object Segmentation in Deep Learning

Object recognition has been widely investigated in computer vision for many years. Currently, this process is carried out through neural networks, but there are very few public datasets available with mask and class labels of the objects for the training process in usual applications. In this paper, we address the problem of fast generation of synthetic datasets to train neural models because creating a handcraft labeled dataset with object segmentation is a very tedious and time-consuming task. We propose an efficient method to generate a synthetic labeled dataset that adequately combines background images with foreground segmented objects. The synthetic images can be created automatically with random positioning of the objects or, alternatively, the method can produce realistic images by keeping the realism in the scales and positions of the objects. Then, we employ Mask-RCNN deep learning model, to detect and segment classes of kitchen objects using images. In the experimental evaluation, we study both synthetic datasets, automatic or realistic, and we compare the results. We analyze the performance with the most widely used indexes and check that the realistic synthetic dataset, quickly created through our method, can provide competitive results and accurately classify the different objects

A Comprehensive Overview of Computational Nuclei Segmentation Methods in Digital Pathology

In the cancer diagnosis pipeline, digital pathology plays an instrumental role in the identification, staging, and grading of malignant areas on biopsy tissue specimens. High resolution histology images are subject to high variance in appearance, sourcing either from the acquisition devices or the H\&E staining process. Nuclei segmentation is an important task, as it detects the nuclei cells over background tissue and gives rise to the topology, size, and count of nuclei which are determinant factors for cancer detection. Yet, it is a fairly time consuming task for pathologists, with reportedly high subjectivity. Computer Aided Diagnosis (CAD) tools empowered by modern Artificial Intelligence (AI) models enable the automation of nuclei segmentation. This can reduce the subjectivity in analysis and reading time. This paper provides an extensive review, beginning from earlier works use traditional image processing techniques and reaching up to modern approaches following the Deep Learning (DL) paradigm. Our review also focuses on the weak supervision aspect of the problem, motivated by the fact that annotated data is scarce. At the end, the advantages of different models and types of supervision are thoroughly discussed. Furthermore, we try to extrapolate and envision how future research lines will potentially be, so as to minimize the need for labeled data while maintaining high performance. Future methods should emphasize efficient and explainable models with a transparent underlying process so that physicians can trust their output.Comment: 47 pages, 27 figures, 9 table

Optimizing Deep Neural Networks for Single Cell Segmentation

Analysis of live-cell imaging experiments at the resolution of single cells provides exciting insights into the inner workings of biological systems. Advances in biological imaging and computer vision allow for segmentation of natural images with a high degree of accuracy. However, automation of the segmentation pipeline at the single cell resolution remains a challenging task. Complex deep learning models require large, well-annotated datasets that are rarely available in biology. In this research, we explore various methods that optimize state of the art deep learning frameworks, despite limited resources. We trained a large permutation of models to quantify their capacity and to measure the effects of temporal information, spatial awareness and transfer learning on model performance. We find that, although training set size is most impactful in improving model accuracy, we can leverage techniques like spatial awareness and transfer learning to compromise for the lack of data. These insights show that, with an abundance of data, light-weight models can be as performant as their heavy-weight counterparts in cellular analysis

A Comparison of Deep Learning Algorithms on Image Data for Detecting Floodwater on Roadways

Object detection and segmentation algorithms evolved significantly in the last decade. Simultaneous object detection and segmentation paved the way for real-time applications such as autonomous driving. Detection and segmentation of (partially) flooded roadways are essential inputs for vehicle routing and traffic management systems. This paper proposes an automatic floodwater detection and segmentation method utilizing the Mask Region-Based Convolutional Neural Networks (Mask-R-CNN) and Generative Adversarial Networks (GAN) algorithms. To train the model, manually labeled images with urban, suburban, and natural settings are used. The performances of the algorithms are assessed in accurately detecting the floodwater captured in images. The results show that the proposed Mask-R-CNN-based floodwater detection and segmentation outperform previous studies, whereas the GAN-based model has a straightforward implementation compared to other models

Active Learning Pipeline for Brain Mapping in a High Performance Computing Environment

This paper describes a scalable active learning pipeline prototype for large-scale brain mapping that leverages high performance computing power. It enables high-throughput evaluation of algorithm results, which, after human review, are used for iterative machine learning model training. Image processing and machine learning are performed in a batch layer. Benchmark testing of image processing using pMATLAB shows that a 100$\times$ increase in throughput (10,000%) can be achieved while total processing time only increases by 9% on Xeon-G6 CPUs and by 22% on Xeon-E5 CPUs, indicating robust scalability. The images and algorithm results are provided through a serving layer to a browser-based user interface for interactive review. This pipeline has the potential to greatly reduce the manual annotation burden and improve the overall performance of machine learning-based brain mapping.Comment: 6 pages, 5 figures, submitted to IEEE HPEC 2020 proceeding

Segmentation in large-scale cellular electron microscopy with deep learning: A literature survey

Electron microscopy (EM) enables high-resolution imaging of tissues and cells based on 2D and 3D imaging techniques. Due to the laborious and time-consuming nature of manual segmentation of large-scale EM datasets, automated segmentation approaches are crucial. This review focuses on the progress of deep learning-based segmentation techniques in large-scale cellular EM throughout the last six years, during which significant progress has been made in both semantic and instance segmentation. A detailed account is given for the key datasets that contributed to the proliferation of deep learning in 2D and 3D EM segmentation. The review covers supervised, unsupervised, and self-supervised learning methods and examines how these algorithms were adapted to the task of segmenting cellular and sub-cellular structures in EM images. The special challenges posed by such images, like heterogeneity and spatial complexity, and the network architectures that overcame some of them are described. Moreover, an overview of the evaluation measures used to benchmark EM datasets in various segmentation tasks is provided. Finally, an outlook of current trends and future prospects of EM segmentation is given, especially with large-scale models and unlabeled images to learn generic features across EM datasets