A Petri Dish for Histopathology Image Analysis

• URL: http://arxiv.org/abs/2101.12355v1
• Date: Fri, 29 Jan 2021 02:01:45 GMT
• Title: A Petri Dish for Histopathology Image Analysis
• Authors: Jerry Wei and Arief Suriawinata and Bing Ren and Xiaoying Liu and Mikhail Lisovsky and Louis Vaickus and Charles Brown and Michael Baker and Naofumi Tomita and Lorenzo Torresani and Jason Wei and Saeed Hassanpour
• Abstract summary: We introduce a minimalist histopathology image analysis dataset (MHIST) MHIST is a binary classification dataset of 3,152 fixed-size images of colorectal polyps. MHIST occupies less than 400 MB of disk space, and a ResNet-18 baseline can be trained to convergence on MHIST in just 6 minutes.
• Score: 25.424907516487327
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: With the rise of deep learning, there has been increased interest in using neural networks for histopathology image analysis, a field that investigates the properties of biopsy or resected specimens that are traditionally manually examined under a microscope by pathologists. In histopathology image analysis, however, challenges such as limited data, costly annotation, and processing high-resolution and variable-size images create a high barrier of entry and make it difficult to quickly iterate over model designs. Throughout scientific history, many significant research directions have leveraged small-scale experimental setups as petri dishes to efficiently evaluate exploratory ideas, which are then validated in large-scale applications. For instance, the Drosophila fruit fly in genetics and MNIST in computer vision are well-known petri dishes. In this paper, we introduce a minimalist histopathology image analysis dataset (MHIST), an analogous petri dish for histopathology image analysis. MHIST is a binary classification dataset of 3,152 fixed-size images of colorectal polyps, each with a gold-standard label determined by the majority vote of seven board-certified gastrointestinal pathologists and annotator agreement level. MHIST occupies less than 400 MB of disk space, and a ResNet-18 baseline can be trained to convergence on MHIST in just 6 minutes using 3.5 GB of memory on a NVIDIA RTX 3090. As example use cases, we use MHIST to study natural questions such as how dataset size, network depth, transfer learning, and high-disagreement examples affect model performance. By introducing MHIST, we hope to not only help facilitate the work of current histopathology imaging researchers, but also make histopathology image analysis more accessible to the general computer vision community. Our dataset is available at https://bmirds.github.io/MHIST.

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