Zeeshan Nisar

Zeeshan Nisar, Friedrich Feuerhake, Thomas Lampert

A key challenge in segmentation in digital histopathology is inter- and intra-stain variations as it reduces model performance. Labelling each stain is expensive and time-consuming so methods using stain transfer via CycleGAN, have been developed for training multi-stain segmentation models using labels from a single stain. Nevertheless, CycleGAN tends to introduce noise during translation because of the one-to-many nature of some stain pairs, which conflicts with its cycle consistency loss. To address this, we propose the Domain Shift Aware CycleGAN, which reduces the presence of such noise. Furthermore, we evaluate several advances from the field of machine learning aimed at resolving similar problems and compare their effectiveness against DSA-CycleGAN in the context of multi-stain glomeruli segmentation. Experiments demonstrate that DSA-CycleGAN not only improves segmentation performance in glomeruli segmentation but also outperforms other methods in reducing noise. This is particularly evident when translating between biologically distinct stains. The code is publicly available at https://github.com/zeeshannisar/DSA-CycleGAN.

Zeeshan Nisar, Jelica Vasiljević, Pierre Gançarski et al.

Domain shift in digital histopathology can occur when different stains or scanners are used, during stain translation, etc. A deep neural network trained on source data may not generalise well to data that has undergone some domain shift. An important step towards being robust to domain shift is the ability to detect and measure it. This article demonstrates that the PixelCNN and domain shift metric can be used to detect and quantify domain shift in digital histopathology, and they demonstrate a strong correlation with generalisation performance. These findings pave the way for a mechanism to infer the average performance of a model (trained on source data) on unseen and unlabelled target data.

Tehseen Zia, Zeeshan Nisar, Shakeeb Murtaza

The image-based diagnosis is now a vital aspect of modern automation assisted diagnosis. To enable models to produce pixel-level diagnosis, pixel-level ground-truth labels are essentially required. However, since it is often not straight forward to obtain the labels in many application domains such as in medical image, classification-based approaches have become the de facto standard to perform the diagnosis. Though they can identify class-salient regions, they may not be useful for diagnosis where capturing all of the evidences is important requirement. Alternatively, a counterfactual explanation (CX) aims at providing explanations using a casual reasoning process of form "If X has not happend, Y would not heppend". Existing CX approaches, however, use classifier to explain features that can change its predictions. Thus, they can only explain class-salient features, rather than entire object of interest. This hence motivates us to propose a novel CX strategy that is not reliant on image classification. This work is inspired from the recent developments in generative adversarial networks (GANs) based image-to-image domain translation, and leverages to translate an abnormal image to counterpart normal image (i.e. counterfactual instance CI) to find discrepancy maps between the two. Since it is generally not possible to obtain abnormal and normal image pairs, we leverage Cycle-Consistency principle (a.k.a CycleGAN) to perform the translation in unsupervised way. We formulate CX in terms of a discrepancy map that, when added from the abnormal image, will make it indistinguishable from the CI. We evaluate our method on three datasets including a synthetic, tuberculosis and BraTS dataset. All these experiments confirm the supremacy of propose method in generating accurate CX and CI.

Zeeshan Nisar, Friedrich Feuerhake, Thomas Lampert

Semantic segmentation under domain shift remains a fundamental challenge in computer vision, particularly when labelled training data is scarce. This challenge is particularly exemplified in histopathology image analysis, where the same tissue structures must be segmented across images captured under different imaging conditions (stains), each representing a distinct visual domain. Traditional deep learning methods like UNet require extensive labels, which is both costly and time-consuming, particularly when dealing with multiple domains (or stains). To mitigate this, various unsupervised domain adaptation based methods such as UDAGAN have been proposed, which reduce the need for labels by requiring only one (source) stain to be labelled. Nonetheless, obtaining source stain labels can still be challenging. This article shows that through self-supervised pre-training -- including SimCLR, BYOL, and a novel approach, HR-CS-CO -- the performance of these segmentation methods (UNet, and UDAGAN) can be retained even with 95% fewer labels. Notably, with self-supervised pre-training and using only 5% labels, the performance drops are minimal: 5.9% for UNet and 6.2% for UDAGAN, averaged over all stains, compared to their respective fully supervised counterparts (without pre-training, using 100% labels). Furthermore, these findings are shown to generalise beyond their training distribution to public benchmark datasets. Implementations and pre-trained models are publicly available \href{https://github.com/zeeshannisar/resource-effecient-multi-stain-kidney-glomeruli-segmentation.git}{online}.

Niklas Kormann, Masoud Ramuz, Zeeshan Nisar et al.

Graph Neural Networks (GNNs) have recently been found to excel in histopathology. However, an important histopathological task, where GNNs have not been extensively explored, is the classification of glomeruli health as an important indicator in nephropathology. This task presents unique difficulties, particularly for the graph construction, i.e., the identification of nodes, edges, and informative features. In this work, we propose a pipeline composed of different traditional and machine learning-based computer vision techniques to identify nodes, edges, and their corresponding features to form a heterogeneous graph. We then proceed to propose a novel heterogeneous GNN architecture for glomeruli classification, called HIEGNet, that integrates both glomeruli and their surrounding immune cells. Hence, HIEGNet is able to consider the immune environment of each glomerulus in its classification. Our HIEGNet was trained and tested on a dataset of Whole Slide Images from kidney transplant patients. Experimental results demonstrate that HIEGNet outperforms several baseline models and generalises best between patients among all baseline models. Our implementation is publicly available at https://github.com/nklsKrmnn/HIEGNet.git.