scholarly journals Towards better digital pathology workflows: programming libraries for high-speed sharpness assessment of Whole Slide Images

2014 ◽  
Vol 9 (S1) ◽  
Author(s):  
David Ameisen ◽  
Christophe Deroulers ◽  
Valérie Perrier ◽  
Fatiha Bouhidel ◽  
Maxime Battistella ◽  
...  
Keyword(s):  
High Speed ◽  
Digital Pathology ◽  
Whole Slide Images

scholarly journals A Digital Pathology Solution to Resolve the Tissue Floater Conundrum

2020 ◽  
Author(s):  
Liron Pantanowitz ◽  
Pamela Michelow ◽  
Scott Hazelhurst ◽  
Shivam Kalra ◽  
Charles Choi ◽  
...  
Keyword(s):  
Digital Pathology ◽  
Primary Diagnosis ◽  
Image Search ◽  
Molecular Tests ◽  
Tissue Identification ◽  
Digital Database ◽  
Glass Slides ◽  
Search Tool ◽  
Hematoxylin And Eosin ◽  
Whole Slide Images

Context.— Pathologists may encounter extraneous pieces of tissue (tissue floaters) on glass slides because of specimen cross-contamination. Troubleshooting this problem, including performing molecular tests for tissue identification if available, is time consuming and often does not satisfactorily resolve the problem. Objective.— To demonstrate the feasibility of using an image search tool to resolve the tissue floater conundrum. Design.— A glass slide was produced containing 2 separate hematoxylin and eosin (H&E)-stained tissue floaters. This fabricated slide was digitized along with the 2 slides containing the original tumors used to create these floaters. These slides were then embedded into a dataset of 2325 whole slide images comprising a wide variety of H&E stained diagnostic entities. Digital slides were broken up into patches and the patch features converted into barcodes for indexing and easy retrieval. A deep learning-based image search tool was employed to extract features from patches via barcodes, hence enabling image matching to each tissue floater. Results.— There was a very high likelihood of finding a correct tumor match for the queried tissue floater when searching the digital database. Search results repeatedly yielded a correct match within the top 3 retrieved images. The retrieval accuracy improved when greater proportions of the floater were selected. The time to run a search was completed within several milliseconds. Conclusions.— Using an image search tool offers pathologists an additional method to rapidly resolve the tissue floater conundrum, especially for those laboratories that have transitioned to going fully digital for primary diagnosis.

scholarly journals Two Ensemble-CNN Approaches for Colorectal Cancer Tissue Type Classification

2021 ◽  
Vol 7 (3) ◽  
pp. 51
Author(s):  
Emanuela Paladini ◽  
Edoardo Vantaggiato ◽  
Fares Bougourzi ◽  
Cosimo Distante ◽  
Abdenour Hadid ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Deep Learning ◽  
Digital Pathology ◽  
Texture Features ◽  
Tissue Type ◽  
Cancer Tissue ◽  
Learning Methods ◽  
Feature Based ◽  
Type Classification ◽  
Whole Slide Images

In recent years, automatic tissue phenotyping has attracted increasing interest in the Digital Pathology (DP) field. For Colorectal Cancer (CRC), tissue phenotyping can diagnose the cancer and differentiate between different cancer grades. The development of Whole Slide Images (WSIs) has provided the required data for creating automatic tissue phenotyping systems. In this paper, we study different hand-crafted feature-based and deep learning methods using two popular multi-classes CRC-tissue-type databases: Kather-CRC-2016 and CRC-TP. For the hand-crafted features, we use two texture descriptors (LPQ and BSIF) and their combination. In addition, two classifiers are used (SVM and NN) to classify the texture features into distinct CRC tissue types. For the deep learning methods, we evaluate four Convolutional Neural Network (CNN) architectures (ResNet-101, ResNeXt-50, Inception-v3, and DenseNet-161). Moreover, we propose two Ensemble CNN approaches: Mean-Ensemble-CNN and NN-Ensemble-CNN. The experimental results show that the proposed approaches outperformed the hand-crafted feature-based methods, CNN architectures and the state-of-the-art methods in both databases.

scholarly journals A deep-learning-based prognostic nomogram integrating microscopic digital pathology and macroscopic magnetic resonance images in nasopharyngeal carcinoma: a multi-cohort study

2020 ◽  
Vol 12 ◽  
pp. 175883592097141
Author(s):  
Fan Zhang ◽  
Lian-Zhen Zhong ◽  
Xun Zhao ◽  
Di Dong ◽  
Ji-Jin Yao ◽  
...  
Keyword(s):  
Deep Learning ◽  
Magnetic Resonance ◽  
Nasopharyngeal Carcinoma ◽  
Treatment Failure ◽  
Digital Pathology ◽  
Imaging Features ◽  
Multi Scale ◽  
External Test ◽  
Whole Slide Images ◽  
Independent Cohort

Background: To explore the prognostic value of radiomics-based and digital pathology-based imaging biomarkers from macroscopic magnetic resonance imaging (MRI) and microscopic whole-slide images for patients with nasopharyngeal carcinoma (NPC). Methods: We recruited 220 NPC patients and divided them into training ( n = 132), internal test ( n = 44), and external test ( n = 44) cohorts. The primary endpoint was failure-free survival (FFS). Radiomic features were extracted from pretreatment MRI and selected and integrated into a radiomic signature. The histopathological signature was extracted from whole-slide images of biopsy specimens using an end-to-end deep-learning method. Incorporating two signatures and independent clinical factors, a multi-scale nomogram was constructed. We also tested the correlation between the key imaging features and genetic alternations in an independent cohort of 16 patients (biological test cohort). Results: Both radiomic and histopathologic signatures presented significant associations with treatment failure in the three cohorts (C-index: 0.689–0.779, all p < 0.050). The multi-scale nomogram showed a consistent significant improvement for predicting treatment failure compared with the clinical model in the training (C-index: 0.817 versus 0.730, p < 0.050), internal test (C-index: 0.828 versus 0.602, p < 0.050) and external test (C-index: 0.834 versus 0.679, p < 0.050) cohorts. Furthermore, patients were stratified successfully into two groups with distinguishable prognosis (log-rank p < 0.0010) using our nomogram. We also found that two texture features were related to the genetic alternations of chromatin remodeling pathways in another independent cohort. Conclusion: The multi-scale imaging features showed a complementary value in prognostic prediction and may improve individualized treatment in NPC.

scholarly journals Adaptive Localization of Focus Point Regions via Random Patch Probabilistic Density from Whole-Slide, Ki-67-Stained Brain Tumor Tissue

2015 ◽  
Vol 2015 ◽  
pp. 1-13 ◽  
Author(s):  
Yazan M. Alomari ◽  
Siti Norul Huda Sheikh Abdullah ◽  
Reena Rahayu MdZin ◽  
Khairuddin Omar
Keyword(s):  
False Positive Rate ◽  
Digital Pathology ◽  
Clustering Methods ◽  
Ki 67 ◽  
Localization Accuracy ◽  
Density Method ◽  
Clustering Problem ◽  
Positive Rate ◽  
Focus Point ◽  
Whole Slide Images

Analysis of whole-slide tissue for digital pathology images has been clinically approved to provide a second opinion to pathologists. Localization of focus points from Ki-67-stained histopathology whole-slide tissue microscopic images is considered the first step in the process of proliferation rate estimation. Pathologists use eye pooling or eagle-view techniques to localize the highly stained cell-concentrated regions from the whole slide under microscope, which is called focus-point regions. This procedure leads to a high variety of interpersonal observations and time consuming, tedious work and causes inaccurate findings. The localization of focus-point regions can be addressed as a clustering problem. This paper aims to automate the localization of focus-point regions from whole-slide images using the random patch probabilistic density method. Unlike other clustering methods, random patch probabilistic density method can adaptively localize focus-point regions without predetermining the number of clusters. The proposed method was compared with thek-means and fuzzyc-means clustering methods. Our proposed method achieves a good performance, when the results were evaluated by three expert pathologists. The proposed method achieves an average false-positive rate of 0.84% for the focus-point region localization error. Moreover, regarding RPPD used to localize tissue from whole-slide images, 228 whole-slide images have been tested; 97.3% localization accuracy was achieved.

scholarly journals Augmented Reality Technology Using Microsoft HoloLens in Anatomic Pathology

2018 ◽  
Vol 142 (5) ◽  
pp. 638-644 ◽  
Author(s):  
Matthew G. Hanna ◽  
Ishtiaque Ahmed ◽  
Jeffrey Nine ◽  
Shyam Prajapati ◽  
Liron Pantanowitz
Keyword(s):  
Augmented Reality ◽  
Real Time ◽  
Mixed Reality ◽  
Digital Pathology ◽  
Remote Supervision ◽  
Augmented Reality Technology ◽  
Microsoft Hololens ◽  
Microscopic Pathology ◽  
Areas Of Interest ◽  
Whole Slide Images

Context Augmented reality (AR) devices such as the Microsoft HoloLens have not been well used in the medical field. Objective To test the HoloLens for clinical and nonclinical applications in pathology. Design A Microsoft HoloLens was tested for virtual annotation during autopsy, viewing 3D gross and microscopic pathology specimens, navigating whole slide images, telepathology, as well as real-time pathology-radiology correlation. Results Pathology residents performing an autopsy wearing the HoloLens were remotely instructed with real-time diagrams, annotations, and voice instruction. 3D-scanned gross pathology specimens could be viewed as holograms and easily manipulated. Telepathology was supported during gross examination and at the time of intraoperative consultation, allowing users to remotely access a pathologist for guidance and to virtually annotate areas of interest on specimens in real-time. The HoloLens permitted radiographs to be coregistered on gross specimens and thereby enhanced locating important pathologic findings. The HoloLens also allowed easy viewing and navigation of whole slide images, using an AR workstation, including multiple coregistered tissue sections facilitating volumetric pathology evaluation. Conclusions The HoloLens is a novel AR tool with multiple clinical and nonclinical applications in pathology. The device was comfortable to wear, easy to use, provided sufficient computing power, and supported high-resolution imaging. It was useful for autopsy, gross and microscopic examination, and ideally suited for digital pathology. Unique applications include remote supervision and annotation, 3D image viewing and manipulation, telepathology in a mixed-reality environment, and real-time pathology-radiology correlation.

scholarly journals COMPARATIVE FEATURES OF OPEN SOURCE SOFTWARE PRODUCTS FOR THE DEVELOPMENT OF AN AUTOMATED BREAST CANCER DIAGNOSTIC PROGRAM

2019 ◽  
Vol 7 (4) ◽  
pp. 377-385
Author(s):  
V. Kovalev ◽  
Y. Diachenko ◽  
V. Malyshev ◽  
S. Rjabceva ◽  
O. Kolomiets ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Open Source ◽  
Cancer Diagnosis ◽  
Open Source Software ◽  
Imaging Techniques ◽  
Digital Pathology ◽  
Third Party ◽  
Histopathological Diagnosis ◽  
Histological Verification ◽  
Whole Slide Images

Breast cancer is one of the most common cancer diseases in the world among women. The reliability of histological verification of breast cancer depends on pathologist’s experience, knowledge, his willingness to self-improve and study specialized literature. Digital pathology is also widely used for educational purposes, in telepathology, teleconsultation and research projects. Recently developed Whole Slide Image (WSI) system opens great opportunities in the histopathological diagnosis quality improvement. Digital whole-slide images provide the effective use of morphometry and various imaging techniques to assist pathologists in quantitative and qualitative evaluation of histopathological preparations. The development of software for morphological diagnosis is important for improving the quality of histological verification of diagnosis in oncopathology. The purpose of this work is to find and benchmark existing open-source software for the whole-slide histological images processing. Choosing an open source program is an important step in developing an automated breast cancer diagnosis program. The result is a detailed study of open-source software: ASAP, Orbit, Cytomine and QuPath. Their features and methods of image processing were analyzed. QuPath software has the best characteristics for extending it with an automated module for the cancer diagnosis. QuPath combines a user-friendly, easy-to-use interface, customizable functionality, and moderate computing power requirements. Besides, QuPath works with whole-slide images with immunohistochemical markers; features implemented in this software allow making a morphometric analysis. QuPath saves time for a graphical user interface development and provides a scalable system to add new key features. QuPath supports third-party MATLAB and Python extensions.

scholarly journals Reproducibility and Feasibility of Strategies for Morphologic Assessment of Renal Biopsies Using the Nephrotic Syndrome Study Network Digital Pathology Scoring System

2018 ◽  
Vol 142 (5) ◽  
pp. 613-625 ◽  
Author(s):  
Jarcy Zee ◽  
Jeffrey B. Hodgin ◽  
Laura H. Mariani ◽  
Joseph P. Gaut ◽  
Matthew B. Palmer ◽  
...  
Keyword(s):  
Nephrotic Syndrome ◽  
Scoring System ◽  
Digital Pathology ◽  
Published Data ◽  
Renal Biopsies ◽  
Agreement Coefficient ◽  
Continuous Measures ◽  
Level 2 ◽  
Whole Slide Images ◽  
Glomerular Morphology

Context Testing reproducibility is critical for the development of methodologies for morphologic assessment. Our previous study using the descriptor-based Nephrotic Syndrome Study Network Digital Pathology Scoring System (NDPSS) on glomerular images revealed variable reproducibility. Objective To test reproducibility and feasibility of alternative scoring strategies for digital morphologic assessment of glomeruli and explore use of alternative agreement statistics. Design The original NDPSS was modified (NDPSS1 and NDPSS2) to evaluate (1) independent scoring of each individual biopsy level, (2) use of continuous measures, (3) groupings of individual descriptors into classes and subclasses prior to scoring, and (4) indication of pathologists' confidence/uncertainty for any given score. Three and 5 pathologists scored 157 and 79 glomeruli using the NDPSS1 and NDPSS2, respectively. Agreement was tested using conventional (Cohen κ) and alternative (Gwet agreement coefficient 1 [AC1]) agreement statistics and compared with previously published data (original NDPSS). Results Overall, pathologists' uncertainty was low, favoring application of the Gwet AC1. Greater agreement was achieved using the Gwet AC1 compared with the Cohen κ across all scoring methodologies. Mean (standard deviation) differences in agreement estimates using the NDPSS1 and NDPSS2 compared with the single-level original NDPSS were −0.09 (0.17) and −0.17 (0.17), respectively. Using the Gwet AC1, 79% of the original NDPSS descriptors had good or excellent agreement. Pathologist feedback indicated the NDPSS1 and NDPSS2 were time-consuming. Conclusions The NDPSS1 and NDPSS2 increased pathologists' scoring burden without improving reproducibility. Use of alternative agreement statistics was strongly supported. We suggest using the original NDPSS on whole slide images for glomerular morphology assessment and for guiding future automated technologies.

scholarly journals Tissue Type Recognition in Whole Slide Histological Images

2021 ◽  
Author(s):  
Alexander Khvostikov ◽  
Andrey Krylov ◽  
Ilya Mikhailov ◽  
Pavel Malkov ◽  
Natalya Danilova
Keyword(s):  
Digestive Tract ◽  
Lamina Propria ◽  
Gastric Adenocarcinoma ◽  
Digital Pathology ◽  
Tissue Type ◽  
Depth Of Invasion ◽  
Tubular Structures ◽  
Urgent Task ◽  
Histological Images ◽  
Whole Slide Images

Automatic layers recognition of the wall of the stomach and colon on whole slide images is an extremely urgent task in digital pathology as it can be used for automatic determining the depth of invasion of the digestive tract tumors. In this paper we propose a new CNN-based method of automatic tissue type recognition on whole slide histological images. We also describe an effective pipeline of training that uses 2 different training datasets. The proposed method of automatic tissue type recognition achieved 0.929 accuracy and 0.903 balanced accuracy on CRC-VAL-HE-7K dataset for 9-types classification and 0.98 accuracy and 0.926 balanced accuracy on the test subset of whole slide images from PATH-DT- MSU dataset for 5-types classification. The developed method makes it possible to classify the areas corresponding to the gastric own mucous glands in the lamina propria and also to distinguish the tubular structures of a highly differentiated gastric adenocarcinoma with normal glands.

scholarly journals Digital Whole Slide Imaging Compared With Light Microscopy for Primary Diagnosis in Surgical Pathology

2020 ◽  
Vol 144 (10) ◽  
pp. 1245-1253 ◽  
Author(s):  
Alexander D. Borowsky ◽  
Eric F. Glassy ◽  
William Dean Wallace ◽  
Nathash S. Kallichanda ◽  
Cynthia A. Behling ◽  
...  
Keyword(s):  
Digital Pathology ◽  
Diagnostic Category ◽  
Primary Diagnosis ◽  
Current Standard ◽  
Diagnostic Categories ◽  
Standard Glass ◽  
Specific Subset ◽  
Glass Slides ◽  
Major Discrepancy ◽  
Whole Slide Images

Context.— The adoption of digital capture of pathology slides as whole slide images (WSI) for educational and research applications has proven utility. Objective.— To compare pathologists' primary diagnoses derived from WSI versus the standard microscope. Because WSIs differ in format and method of observation compared with the current standard glass slide microscopy, this study is critical to potential clinical adoption of digital pathology. Design.— The study enrolled a total of 2045 cases enriched for more difficult diagnostic categories and represented as 5849 slides were curated and provided for diagnosis by a team of 19 reading pathologists separately as WSI or as glass slides viewed by light microscope. Cases were reviewed by each pathologist in both modalities in randomized order with a minimum 31-day washout between modality reads for each case. Each diagnosis was compared with the original clinical reference diagnosis by an independent central adjudication review. Results.— The overall major discrepancy rates were 3.64% for WSI review and 3.20% for manual slide review diagnosis methods, a difference of 0.44% (95% CI, −0.15 to 1.03). The time to review a case averaged 5.20 minutes for WSI and 4.95 minutes for glass slides. There was no specific subset of diagnostic category that showed higher rates of modality-specific discrepancy, though some categories showed greater discrepancy than others in both modalities. Conclusions.— WSIs are noninferior to traditional glass slides for primary diagnosis in anatomic pathology.

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