21 research outputs found
Rotation Invariance and Extensive Data Augmentation: A Strategy for the MItosis DOmain Generalization (MIDOG) Challenge
Automated detection of mitotic figures in histopathology images is a challenging task: here, we present the different steps that describe the strategy we applied to participate in the MIDOG 2021 competition. The purpose of the competition was to evaluate the generalization of solutions to images acquired with unseen target scanners (hidden for the participants) under the constraint of using training data from a limited set of four independent source scanners. Given this goal and constraints, we joined the challenge by proposing a straight-forward solution based on a combination of state-of-the-art deep learning methods with the aim of yielding robustness to possible scanner-related distributional shifts at inference time. Our solution combines methods that were previously shown to be efficient for mitosis detection: hard negative mining, extensive data augmentation, rotation-invariant convolutional networks.
We trained five models with different splits of the provided dataset. The subsequent classifiers produced F1-score with a mean and standard deviation of 0.747±0.032
on the test splits. The resulting ensemble constitutes our candidate algorithm: its automated evaluation on the preliminary test set of the challenge returned a F1-score of 0.6828
Domain-adversarial neural networks to address the appearance variability of histopathology images
Preparing and scanning histopathology slides consists of several steps, each
with a multitude of parameters. The parameters can vary between pathology labs
and within the same lab over time, resulting in significant variability of the
tissue appearance that hampers the generalization of automatic image analysis
methods. Typically, this is addressed with ad-hoc approaches such as staining
normalization that aim to reduce the appearance variability. In this paper, we
propose a systematic solution based on domain-adversarial neural networks. We
hypothesize that removing the domain information from the model representation
leads to better generalization. We tested our hypothesis for the problem of
mitosis detection in breast cancer histopathology images and made a comparative
analysis with two other approaches. We show that combining color augmentation
with domain-adversarial training is a better alternative than standard
approaches to improve the generalization of deep learning methods.Comment: MICCAI 2017 Workshop on Deep Learning in Medical Image Analysi
Inferring a Third Spatial Dimension from 2D Histological Images
Histological images are obtained by transmitting light through a tissue
specimen that has been stained in order to produce contrast. This process
results in 2D images of the specimen that has a three-dimensional structure. In
this paper, we propose a method to infer how the stains are distributed in the
direction perpendicular to the surface of the slide for a given 2D image in
order to obtain a 3D representation of the tissue. This inference is achieved
by decomposition of the staining concentration maps under constraints that
ensure realistic decomposition and reconstruction of the original 2D images.
Our study shows that it is possible to generate realistic 3D images making this
method a potential tool for data augmentation when training deep learning
models.Comment: IEEE International Symposium on Biomedical Imaging (ISBI), 201
Roto-Translation Equivariant Convolutional Networks: Application to Histopathology Image Analysis
Rotation-invariance is a desired property of machine-learning models for
medical image analysis and in particular for computational pathology
applications. We propose a framework to encode the geometric structure of the
special Euclidean motion group SE(2) in convolutional networks to yield
translation and rotation equivariance via the introduction of SE(2)-group
convolution layers. This structure enables models to learn feature
representations with a discretized orientation dimension that guarantees that
their outputs are invariant under a discrete set of rotations. Conventional
approaches for rotation invariance rely mostly on data augmentation, but this
does not guarantee the robustness of the output when the input is rotated. At
that, trained conventional CNNs may require test-time rotation augmentation to
reach their full capability. This study is focused on histopathology image
analysis applications for which it is desirable that the arbitrary global
orientation information of the imaged tissues is not captured by the machine
learning models. The proposed framework is evaluated on three different
histopathology image analysis tasks (mitosis detection, nuclei segmentation and
tumor classification). We present a comparative analysis for each problem and
show that consistent increase of performances can be achieved when using the
proposed framework
Deep learning supported mitoses counting on whole slide images: A pilot study for validating breast cancer grading in the clinical workflow
INTRODUCTION: Breast cancer (BC) prognosis is largely influenced by histopathological grade, assessed according to the Nottingham modification of Bloom-Richardson (BR). Mitotic count (MC) is a component of histopathological grading but is prone to subjectivity. This study investigated whether mitoses counting in BC using digital whole slide images (WSI) compares better to light microscopy (LM) when assisted by artificial intelligence (AI), and to which extent differences in digital MC (AI assisted or not) result in BR grade variations. METHODS: Fifty BC patients with paired core biopsies and resections were randomly selected. Component scores for BR grade were extracted from pathology reports. MC was assessed using LM, WSI, and AI. Different modalities (LM-MC, WSI-MC, and AI-MC) were analyzed for correlation with scatterplots and linear regression, and for agreement in final BR with Cohen's κ. RESULTS: MC modalities strongly correlated in both biopsies and resections: LM-MC and WSI-MC (R 2 0.85 and 0.83, respectively), LM-MC and AI-MC (R 2 0.85 and 0.95), and WSI-MC and AI-MC (R 2 0.77 and 0.83). Agreement in BR between modalities was high in both biopsies and resections: LM-MC and WSI-MC (κ 0.93 and 0.83, respectively), LM-MC and AI-MC (κ 0.89 and 0.83), and WSI-MC and AI-MC (κ 0.96 and 0.73). CONCLUSION: This first validation study shows that WSI-MC may compare better to LM-MC when using AI. Agreement between BR grade based on the different mitoses counting modalities was high. These results suggest that mitoses counting on WSI can well be done, and validate the presented AI algorithm for pathologist supervised use in daily practice. Further research is required to advance our knowledge of AI-MC, but it appears at least non-inferior to LM-MC
Image-based consensus molecular subtyping in rectal cancer biopsies and response to neoadjuvant chemoradiotherapy
The development of deep learning (DL) models to predict the consensus molecular subtypes (CMS) from histopathology images (imCMS) is a promising and cost-effective strategy to support patient stratification. Here, we investigate whether imCMS calls generated from whole slide histopathology images (WSIs) of rectal cancer (RC) pre-treatment biopsies are associated with pathological complete response (pCR) to neoadjuvant long course chemoradiotherapy (LCRT) with single agent fluoropyrimidine. DL models were trained to classify WSIs of colorectal cancers stained with hematoxylin and eosin into one of the four CMS classes using a multi-centric dataset of resection and biopsy specimens (n = 1057 WSIs) with paired transcriptional data. Classifiers were tested on a held out RC biopsy cohort (ARISTOTLE) and correlated with pCR to LCRT in an independent dataset merging two RC cohorts (ARISTOTLE, n = 114 and SALZBURG, n = 55 patients). DL models predicted CMS with high classification performance in multiple comparative analyses. In the independent cohorts (ARISTOTLE, SALZBURG), cases with WSIs classified as imCMS1 had a significantly higher likelihood of achieving pCR (OR = 2.69, 95% CI 1.01–7.17, p = 0.048). Conversely, imCMS4 was associated with lack of pCR (OR = 0.25, 95% CI 0.07–0.88, p = 0.031). Classification maps demonstrated pathologist-interpretable associations with high stromal content in imCMS4 cases, associated with poor outcome. No significant association was found in imCMS2 or imCMS3. imCMS classification of pre-treatment biopsies is a fast and inexpensive solution to identify patient groups that could benefit from neoadjuvant LCRT. The significant associations between imCMS1/imCMS4 with pCR suggest the existence of predictive morphological features that could enhance standard pathological assessment
Transcriptomics and proteomics reveal distinct biology for lymph node metastases and tumour deposits in colorectal cancer
Both lymph node metastases (LNMs) and tumour deposits (TDs) are included in colorectal cancer (CRC) staging, although knowledge regarding their biological background is lacking. This study aimed to compare the biology of these prognostic features, which is essential for a better understanding of their role in CRC spread. Spatially resolved transcriptomic analysis using digital spatial profiling was performed on TDs and LNMs from 10 CRC patients using 1,388 RNA targets, for the tumour cells and tumour microenvironment. Shotgun proteomics identified 5,578 proteins in 12 different patients. Differences in RNA and protein expression were analysed, and spatial deconvolution was performed. Image-based consensus molecular subtype (imCMS) analysis was performed on all TDs and LNMs included in the study. Transcriptome and proteome profiles identified distinct clusters for TDs and LNMs in both the tumour and tumour microenvironment segment, with upregulation of matrix remodelling, cell adhesion/motility, and epithelial-mesenchymal transition (EMT) in TDs (all p < 0.05). Spatial deconvolution showed a significantly increased abundance of fibroblasts, macrophages, and regulatory T-cells (p < 0.05) in TDs. Consistent with a higher fibroblast and EMT component, imCMS classified 62% of TDs as poor prognosis subtype CMS4 compared to 36% of LNMs (p < 0.05). Compared to LNMs, TDs have a more invasive state involving a distinct tumour microenvironment and upregulation of EMT, which are reflected in a more frequent histological classification of TDs as CMS4. These results emphasise the heterogeneity of locoregional spread and the fact that TDs should merit more attention both in future research and during staging. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland
Mitosis domain generalization in histopathology images -- The MIDOG challenge
The density of mitotic figures within tumor tissue is known to be highly
correlated with tumor proliferation and thus is an important marker in tumor
grading. Recognition of mitotic figures by pathologists is known to be subject
to a strong inter-rater bias, which limits the prognostic value.
State-of-the-art deep learning methods can support the expert in this
assessment but are known to strongly deteriorate when applied in a different
clinical environment than was used for training. One decisive component in the
underlying domain shift has been identified as the variability caused by using
different whole slide scanners. The goal of the MICCAI MIDOG 2021 challenge has
been to propose and evaluate methods that counter this domain shift and derive
scanner-agnostic mitosis detection algorithms. The challenge used a training
set of 200 cases, split across four scanning systems. As a test set, an
additional 100 cases split across four scanning systems, including two
previously unseen scanners, were given. The best approaches performed on an
expert level, with the winning algorithm yielding an F_1 score of 0.748 (CI95:
0.704-0.781). In this paper, we evaluate and compare the approaches that were
submitted to the challenge and identify methodological factors contributing to
better performance.Comment: 19 pages, 9 figures, summary paper of the 2021 MICCAI MIDOG challeng
Pathway level subtyping identifies a slow-cycling biological phenotype associated with poor clinical outcomes in colorectal cancer
Molecular stratification using gene-level transcriptional data has identified subtypes with distinctive genotypic and phenotypic traits, as exemplified by the consensus molecular subtypes (CMS) in colorectal cancer (CRC). Here, rather than gene-level data, we make use of gene ontology and biological activation state information for initial molecular class discovery. In doing so, we defined three pathway-derived subtypes (PDS) in CRC: PDS1 tumors, which are canonical/LGR5+ stem-rich, highly proliferative and display good prognosis; PDS2 tumors, which are regenerative/ANXA1+ stem-rich, with elevated stromal and immune tumor microenvironmental lineages; and PDS3 tumors, which represent a previously overlooked slow-cycling subset of tumors within CMS2 with reduced stem populations and increased differentiated lineages, particularly enterocytes and enteroendocrine cells, yet display the worst prognosis in locally advanced disease. These PDS3 phenotypic traits are evident across numerous bulk and single-cell datasets, and demark a series of subtle biological states that are currently under-represented in pre-clinical models and are not identified using existing subtyping classifiers