Ansh Kapil

Felix Jakob Segerer, Katharina Nekolla, Lorenz Rognoni et al.

Generative Adversarial Networks (GANs) are state of the art for image synthesis. Here, we present dapi2ck, a novel GAN-based approach to synthesize cytokeratin (CK) staining from immunofluorescent (IF) DAPI staining of nuclei in non-small cell lung cancer (NSCLC) images. We use the synthetic CK to segment epithelial regions, which, compared to expert annotations, yield equally good results as segmentation on stained CK. Considering the limited number of markers in a multiplexed IF (mIF) panel, our approach allows to replace CK by another marker addressing the complexity of the tumor micro-environment (TME) to facilitate patient selection for immunotherapies. In contrast to stained CK, dapi2ck does not suffer from issues like unspecific CK staining or loss of tumoral CK expression.

Nicolas Brieu, Felix J. Segerer, Ansh Kapil et al.

Unsupervised and unpaired domain translation using generative adversarial neural networks, and more precisely CycleGAN, is state of the art for the stain translation of histopathology images. It often, however, suffers from the presence of cycle-consistent but non structure-preserving errors. We propose an alternative approach to the set of methods which, relying on segmentation consistency, enable the preservation of pathology structures. Focusing on immunohistochemistry (IHC) and multiplexed immunofluorescence (mIF), we introduce a simple yet effective guidance scheme as a loss function that leverages the consistency of stain translation with stain isolation. Qualitative and quantitative experiments show the ability of the proposed approach to improve translation between the two domains.

Nicolas Brieu, Armin Meier, Ansh Kapil et al.

The detection of nuclei is one of the most fundamental components of computational pathology. Current state-of-the-art methods are based on deep learning, with the prerequisite that extensive labeled datasets are available. The increasing number of patient cohorts to be analyzed, the diversity of tissue stains and indications, as well as the cost of dataset labeling motivates the development of novel methods to reduce labeling effort across domains. We introduce in this work a weakly supervised 'inter-domain' approach that (i) performs stain normalization and unpaired image-to-image translation to transform labeled images on a source domain to synthetic labeled images on an unlabeled target domain and (ii) uses the resulting synthetic labeled images to train a detection network on the target domain. Extensive experiments show the superiority of the proposed approach against the state-of-the-art 'intra-domain' detection based on fully-supervised learning.

Ansh Kapil, Tobias Wiestler, Simon Lanzmich et al.

The analysis of the tumor environment on digital histopathology slides is becoming key for the understanding of the immune response against cancer, supporting the development of novel immuno-therapies. We introduce here a novel deep learning solution to the related problem of tumor epithelium segmentation. While most existing deep learning segmentation approaches are trained on time-consuming and costly manual annotation on single stain domain (PD-L1), we leverage here semi-automatically labeled images from a second stain domain (Cytokeratin-CK). We introduce an end-to-end trainable network that jointly segment tumor epithelium on PD-L1 while leveraging unpaired image-to-image translation between CK and PD-L1, therefore completely bypassing the need for serial sections or re-staining of slides. Extending the method to differentiate between PD-L1 positive and negative tumor epithelium regions enables the automated estimation of the PD-L1 Tumor Cell (TC) score. Quantitative experimental results demonstrate the accuracy of our approach against state-of-the-art segmentation methods.

Christian Rupprecht, Ansh Kapil, Nan Liu et al.

Webly-supervised learning has recently emerged as an alternative paradigm to traditional supervised learning based on large-scale datasets with manual annotations. The key idea is that models such as CNNs can be learned from the noisy visual data available on the web. In this work we aim to exploit web data for video understanding tasks such as action recognition and detection. One of the main problems in webly-supervised learning is cleaning the noisy labeled data from the web. The state-of-the-art paradigm relies on training a first classifier on noisy data that is then used to clean the remaining dataset. Our key insight is that this procedure biases the second classifier towards samples that the first one understands. Here we train two independent CNNs, a RGB network on web images and video frames and a second network using temporal information from optical flow. We show that training the networks independently is vastly superior to selecting the frames for the flow classifier by using our RGB network. Moreover, we show benefits in enriching the training set with different data sources from heterogeneous public web databases. We demonstrate that our framework outperforms all other webly-supervised methods on two public benchmarks, UCF-101 and Thumos'14.