no code implementations • 11 Apr 2024 • Marc Aubreville, Jonathan Ganz, Jonas Ammeling, Christopher C. Kaltenecker, Christof A. Bertram
The QUILT-1M dataset is the first openly available dataset containing images harvested from various online sources.
no code implementations • 15 Nov 2023 • Jonas Ammeling, Moritz Hecker, Jonathan Ganz, Taryn A. Donovan, Christof A. Bertram, Katharina Breininger, Marc Aubreville
The volume-corrected mitotic index (M/V-Index) was shown to provide prognostic value in invasive breast carcinomas.
no code implementations • 27 Sep 2023 • Marc Aubreville, Nikolas Stathonikos, Taryn A. Donovan, Robert Klopfleisch, Jonathan Ganz, Jonas Ammeling, Frauke Wilm, Mitko Veta, Samir Jabari, Markus Eckstein, Jonas Annuscheit, Christian Krumnow, Engin Bozaba, Sercan Cayir, Hongyan Gu, Xiang 'Anthony' Chen, Mostafa Jahanifar, Adam Shephard, Satoshi Kondo, Satoshi Kasai, Sujatha Kotte, VG Saipradeep, Maxime W. Lafarge, Viktor H. Koelzer, Ziyue Wang, Yongbing Zhang, Sen yang, Xiyue Wang, Katharina Breininger, Christof A. Bertram
The challenge provided annotated histologic tumor images from six different domains and evaluated the algorithmic approaches for mitotic figure detection provided by nine challenge participants on ten independent domains.
no code implementations • 26 Sep 2023 • Andreas Haghofer, Eda Parlak, Alexander Bartel, Taryn A. Donovan, Charles-Antoine Assenmacher, Pompei Bolfa, Michael J. Dark, Andrea Fuchs-Baumgartinger, Andrea Klang, Kathrin Jäger, Robert Klopfleisch, Sophie Merz, Barbara Richter, F. Yvonne Schulman, Jonathan Ganz, Josef Scharinger, Marc Aubreville, Stephan M. Winkler, Matti Kiupel, Christof A. Bertram
Algorithmic morphometry was compared with karyomegaly estimates by 11 pathologists, manual nuclear morphometry of 12 cells by 9 pathologists, and the mitotic count as a benchmark.
no code implementations • 31 May 2023 • Christof A. Bertram, Taryn A. Donovan, Alexander Bartel
The goal of this systematic review is to scholarly analyze the methods and prognostic relevance of histologically measuring mitotic activity in canine tumors.
no code implementations • 2 May 2023 • Christof A. Bertram, Taryn A. Donovan, Alexander Bartel
The goal of this systematic review is scholarly analysis of all available references on mitotic activity in feline tumors, and to provide an overview of the measuring methods and prognostic value.
1 code implementation • 11 Jan 2023 • Frauke Wilm, Marco Fragoso, Christof A. Bertram, Nikolas Stathonikos, Mathias Öttl, Jingna Qiu, Robert Klopfleisch, Andreas Maier, Katharina Breininger, Marc Aubreville
Additionally, to quantify the inherent scanner-induced domain shift, we train a tumor segmentation network on each scanner subset and evaluate the performance both in- and cross-domain.
no code implementations • 15 Dec 2022 • Jonathan Ganz, Karoline Lipnik, Jonas Ammeling, Barbara Richter, Chloé Puget, Eda Parlak, Laura Diehl, Robert Klopfleisch, Taryn A. Donovan, Matti Kiupel, Christof A. Bertram, Katharina Breininger, Marc Aubreville
Nucleolar organizer regions (NORs) are parts of the DNA that are involved in RNA transcription.
1 code implementation • 12 Dec 2022 • Marc Aubreville, Jonathan Ganz, Jonas Ammeling, Taryn A. Donovan, Rutger H. J. Fick, Katharina Breininger, Christof A. Bertram
In this work, we perform, for the first time, automatic subtyping of mitotic figures into normal and atypical categories according to characteristic morphological appearances of the different phases of mitosis.
no code implementations • 29 Nov 2022 • Frauke Wilm, Marco Fragoso, Christof A. Bertram, Nikolas Stathonikos, Mathias Öttl, Jingna Qiu, Robert Klopfleisch, Andreas Maier, Marc Aubreville, Katharina Breininger
Computer-aided systems in histopathology are often challenged by various sources of domain shift that impact the performance of these algorithms considerably.
no code implementations • 17 Nov 2022 • Guillaume Balezo, Christof A. Bertram, Cyprien Tilmant, Stéphanie Petit, Saima Ben Hadj, Rutger H. J. Fick
In histology, the presence of collagen in the extra-cellular matrix has both diagnostic and prognostic value for cancer malignancy, and can be highlighted by adding Saffron (S) to a routine Hematoxylin and Eosin (HE) staining.
no code implementations • 6 Apr 2022 • Marc Aubreville, Nikolas Stathonikos, Christof A. Bertram, Robert Klopleisch, Natalie ter Hoeve, Francesco Ciompi, Frauke Wilm, Christian Marzahl, Taryn A. Donovan, Andreas Maier, Jack Breen, Nishant Ravikumar, Youjin Chung, Jinah Park, Ramin Nateghi, Fattaneh Pourakpour, Rutger H. J. Fick, Saima Ben Hadj, Mostafa Jahanifar, Nasir Rajpoot, Jakob Dexl, Thomas Wittenberg, Satoshi Kondo, Maxime W. Lafarge, Viktor H. Koelzer, Jingtang Liang, YuBo Wang, Xi Long, Jingxin Liu, Salar Razavi, April Khademi, Sen yang, Xiyue Wang, Mitko Veta, Katharina Breininger
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.
1 code implementation • 27 Jan 2022 • Frauke Wilm, Marco Fragoso, Christian Marzahl, Jingna Qiu, Chloé Puget, Laura Diehl, Christof A. Bertram, Robert Klopfleisch, Andreas Maier, Katharina Breininger, Marc Aubreville
Due to morphological similarities, the differentiation of histologic sections of cutaneous tumors into individual subtypes can be challenging.
no code implementations • 5 Nov 2021 • Sonja Kunzmann, Christian Marzahl, Felix Denzinger, Christof A. Bertram, Robert Klopfleisch, Katharina Breininger, Vincent Christlein, Andreas Maier
Annotating data, especially in the medical domain, requires expert knowledge and a lot of effort.
1 code implementation • 19 Aug 2021 • Christian Marzahl, Jenny Hill, Jason Stayt, Dorothee Bienzle, Lutz Welker, Frauke Wilm, Jörn Voigt, Marc Aubreville, Andreas Maier, Robert Klopfleisch, Katharina Breininger, Christof A. Bertram
Pulmonary hemorrhage (P-Hem) occurs among multiple species and can have various causes.
1 code implementation • MICCAI Workshop COMPAY 2021 • Jonathan Ganz, Tobias Kirsch, Lucas Hoffmann, Christof A. Bertram, Christoph Hoffmann, Andreas Maier, Katharina Breininger, Ingmar Blümcke, Samir Jabari, Marc Aubreville
In a first approach, image patches are sampled from this region and regression is based on morphological features encoded by a ResNet-based network.
no code implementations • 13 Jan 2021 • Christian Marzahl, Christof A. Bertram, Frauke Wilm, Jörn Voigt, Ann K. Barton, Robert Klopfleisch, Katharina Breininger, Andreas Maier, Marc Aubreville
We evaluated our pipeline in a cross-validation setup with a fixed training set using a dataset of six equine WSIs of which four are partially annotated and used for training, and two fully annotated WSI are used for validation and testing.
2 code implementations • 5 Jan 2021 • Christof A. Bertram, Taryn A. Donovan, Marco Tecilla, Florian Bartenschlager, Marco Fragoso, Frauke Wilm, Christian Marzahl, Katharina Breininger, Andreas Maier, Robert Klopfleisch, Marc Aubreville
For this study, we created the first open source data-set with 19, 983 annotations of BiNC and 1, 416 annotations of MuNC in 32 histological whole slide images of ccMCT.
no code implementations • 4 Dec 2020 • Frauke Wilm, Christof A. Bertram, Christian Marzahl, Alexander Bartel, Taryn A. Donovan, Charles-Antoine Assenmacher, Kathrin Becker, Mark Bennett, Sarah Corner, Brieuc Cossic, Daniela Denk, Martina Dettwiler, Beatriz Garcia Gonzalez, Corinne Gurtner, Annika Lehmbecker, Sophie Merz, Stephanie Plog, Anja Schmidt, Rebecca C. Smedley, Marco Tecilla, Tuddow Thaiwong, Katharina Breininger, Matti Kiupel, Andreas Maier, Robert Klopfleisch, Marc Aubreville
Density of mitotic figures in histologic sections is a prognostically relevant characteristic for many tumours.
1 code implementation • 24 Aug 2020 • Marc Aubreville, Christof A. Bertram, Taryn A. Donovan, Christian Marzahl, Andreas Maier, Robert Klopfleisch
We achieved a mean F1-score of 0. 791 on the test set and of up to 0. 696 on a human breast cancer dataset.
1 code implementation • 10 Jul 2020 • Christof A. Bertram, Mitko Veta, Christian Marzahl, Nikolas Stathonikos, Andreas Maier, Robert Klopfleisch, Marc Aubreville
To date, some datasets on mitotic figures are available and were used for development of promising deep learning-based algorithms.
2 code implementations • 30 Apr 2020 • Christian Marzahl, Marc Aubreville, Christof A. Bertram, Jennifer Maier, Christian Bergler, Christine Kröger, Jörn Voigt, Katharina Breininger, Robert Klopfleisch, Andreas Maier
In many research areas, scientific progress is accelerated by multidisciplinary access to image data and their interdisciplinary annotation.
1 code implementation • 13 Apr 2020 • Christian Marzahl, Christof A. Bertram, Marc Aubreville, Anne Petrick, Kristina Weiler, Agnes C. Gläsel, Marco Fragoso, Sophie Merz, Florian Bartenschlager, Judith Hoppe, Alina Langenhagen, Anne Jasensky, Jörn Voigt, Robert Klopfleisch, Andreas Maier
However, a significant percentage of the deliberately introduced false labels was not identified by the experts.
Human-Computer Interaction Image and Video Processing
no code implementations • 25 Nov 2019 • Marc Aubreville, Christof A. Bertram, Samir Jabari, Christian Marzahl, Robert Klopfleisch, Andreas Maier
We were able to show that domain adversarial training considerably improves accuracy when applying mitotic figure classification learned from the canine on the human data sets (up to +12. 8% in accuracy) and is thus a helpful method to transfer knowledge from existing data sets to new tissue types and species.
2 code implementations • 12 Aug 2019 • Christian Marzahl, Marc Aubreville, Christof A. Bertram, Jason Stayt, Anne-Katherine Jasensky, Florian Bartenschlager, Marco Fragoso-Garcia, Ann K. Barton, Svenja Elsemann, Samir Jabari, Jens Krauth, Prathmesh Madhu, Jörn Voigt, Jenny Hill, Robert Klopfleisch, Andreas Maier
Additionally, we evaluated object detection methods on a novel data set of 17 completely annotated cytology whole slide images (WSI) containing 78, 047 hemosiderophages.
1 code implementation • 12 Feb 2019 • Marc Aubreville, Christof A. Bertram, Christian Marzahl, Corinne Gurtner, Martina Dettwiler, Anja Schmidt, Florian Bartenschlager, Sophie Merz, Marco Fragoso, Olivia Kershaw, Robert Klopfleisch, Andreas Maier
Manual count of mitotic figures, which is determined in the tumor region with the highest mitotic activity, is a key parameter of most tumor grading schemes.
no code implementations • 22 Oct 2018 • Marc Aubreville, Christof A. Bertram, Robert Klopfleisch, Andreas Maier
For both approaches, the CNN performs a segmentation of the WSI to assess mitotic activity.
no code implementations • 1 Oct 2018 • Marc Aubreville, Christof A. Bertram, Robert Klopfleisch, Andreas Maier
This map is in a second step used to construct a mitotic activity estimate.