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Marcel P. Schilling

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CoNIC Challenge: Pushing the Frontiers of Nuclear Detection, Segmentation, Classification and Counting

Mar 14, 2023
Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Martin Weigert, Uwe Schmidt, Wenhua Zhang, Jun Zhang, Sen Yang, Jinxi Xiang, Xiyue Wang, Josef Lorenz Rumberger, Elias Baumann, Peter Hirsch, Lihao Liu, Chenyang Hong, Angelica I. Aviles-Rivero, Ayushi Jain, Heeyoung Ahn, Yiyu Hong, Hussam Azzuni, Min Xu, Mohammad Yaqub, Marie-Claire Blache, Benoît Piégu, Bertrand Vernay, Tim Scherr, Moritz Böhland, Katharina Löffler, Jiachen Li, Weiqin Ying, Chixin Wang, Dagmar Kainmueller, Carola-Bibiane Schönlieb, Shuolin Liu, Dhairya Talsania, Yughender Meda, Prakash Mishra, Muhammad Ridzuan, Oliver Neumann, Marcel P. Schilling, Markus Reischl, Ralf Mikut, Banban Huang, Hsiang-Chin Chien, Ching-Ping Wang, Chia-Yen Lee, Hong-Kun Lin, Zaiyi Liu, Xipeng Pan, Chu Han, Jijun Cheng, Muhammad Dawood, Srijay Deshpande, Raja Muhammad Saad Bashir, Adam Shephard, Pedro Costa, João D. Nunes, Aurélio Campilho, Jaime S. Cardoso, Hrishikesh P S, Densen Puthussery, Devika R G, Jiji C V, Ye Zhang, Zijie Fang, Zhifan Lin, Yongbing Zhang, Chunhui Lin, Liukun Zhang, Lijian Mao, Min Wu, Vi Thi-Tuong Vo, Soo-Hyung Kim, Taebum Lee, Satoshi Kondo, Satoshi Kasai, Pranay Dumbhare, Vedant Phuse, Yash Dubey, Ankush Jamthikar, Trinh Thi Le Vuong, Jin Tae Kwak, Dorsa Ziaei, Hyun Jung, Tianyi Miao, David Snead, Shan E Ahmed Raza, Fayyaz Minhas, Nasir M. Rajpoot

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Nuclear detection, segmentation and morphometric profiling are essential in helping us further understand the relationship between histology and patient outcome. To drive innovation in this area, we setup a community-wide challenge using the largest available dataset of its kind to assess nuclear segmentation and cellular composition. Our challenge, named CoNIC, stimulated the development of reproducible algorithms for cellular recognition with real-time result inspection on public leaderboards. We conducted an extensive post-challenge analysis based on the top-performing models using 1,658 whole-slide images of colon tissue. With around 700 million detected nuclei per model, associated features were used for dysplasia grading and survival analysis, where we demonstrated that the challenge's improvement over the previous state-of-the-art led to significant boosts in downstream performance. Our findings also suggest that eosinophils and neutrophils play an important role in the tumour microevironment. We release challenge models and WSI-level results to foster the development of further methods for biomarker discovery.

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ciscNet -- A Single-Branch Cell Instance Segmentation and Classification Network

Feb 25, 2022
Moritz Böhland, Oliver Neumann, Marcel P. Schilling, Markus Reischl, Ralf Mikut, Katharina Löffler, Tim Scherr

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Automated cell nucleus segmentation and classification are required to assist pathologists in their decision making. The Colon Nuclei Identification and Counting Challenge 2022 (CoNIC Challenge 2022) supports the development and comparability of segmentation and classification methods for histopathological images. In this contribution, we describe our CoNIC Challenge 2022 method ciscNet to segment, classify and count cell nuclei, and report preliminary evaluation results. Our code is available at https://git.scc.kit.edu/ciscnet/ciscnet-conic-2022.

* CoNIC Challenge 2022 submission 
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Label Assistant: A Workflow for Assisted Data Annotation in Image Segmentation Tasks

Nov 27, 2021
Marcel P. Schilling, Luca Rettenberger, Friedrich Münke, Haijun Cui, Anna A. Popova, Pavel A. Levkin, Ralf Mikut, Markus Reischl

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Recent research in the field of computer vision strongly focuses on deep learning architectures to tackle image processing problems. Deep neural networks are often considered in complex image processing scenarios since traditional computer vision approaches are expensive to develop or reach their limits due to complex relations. However, a common criticism is the need for large annotated datasets to determine robust parameters. Annotating images by human experts is time-consuming, burdensome, and expensive. Thus, support is needed to simplify annotation, increase user efficiency, and annotation quality. In this paper, we propose a generic workflow to assist the annotation process and discuss methods on an abstract level. Thereby, we review the possibilities of focusing on promising samples, image pre-processing, pre-labeling, label inspection, or post-processing of annotations. In addition, we present an implementation of the proposal by means of a developed flexible and extendable software prototype nested in hybrid touchscreen/laptop device.

* Proceedings - 31. Workshop Computational Intelligence, 2021  
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Radar Artifact Labeling Framework (RALF): Method for Plausible Radar Detections in Datasets

Dec 03, 2020
Simon T. Isele, Marcel P. Schilling, Fabian E. Klein, Sascha Saralajew, J. Marius Zoellner

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Research on localization and perception for Autonomous Driving is mainly focused on camera and LiDAR datasets, rarely on radar data. Manually labeling sparse radar point clouds is challenging. For a dataset generation, we propose the cross sensor Radar Artifact Labeling Framework (RALF). Automatically generated labels for automotive radar data help to cure radar shortcomings like artifacts for the application of artificial intelligence. RALF provides plausibility labels for radar raw detections, distinguishing between artifacts and targets. The optical evaluation backbone consists of a generalized monocular depth image estimation of surround view cameras plus LiDAR scans. Modern car sensor sets of cameras and LiDAR allow to calibrate image-based relative depth information in overlapping sensing areas. K-Nearest Neighbors matching relates the optical perception point cloud with raw radar detections. In parallel, a temporal tracking evaluation part considers the radar detections' transient behavior. Based on the distance between matches, respecting both sensor and model uncertainties, we propose a plausibility rating of every radar detection. We validate the results by evaluating error metrics on semi-manually labeled ground truth dataset of $3.28\cdot10^6$ points. Besides generating plausible radar detections, the framework enables further labeled low-level radar signal datasets for applications of perception and Autonomous Driving learning tasks.

* pre-print, currently under review 
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