State-of-the-art (SOTA) methods for cell instance segmentation are based on deep learning (DL) semantic segmentation approaches, focusing on distinguishing foreground pixels from background pixels. In order to identify cell instances from foreground pixels (e.g., pixel clustering), most methods decompose instance information into pixel-wise objectives, such as distances to foreground-background boundaries (distance maps), heat gradients with the center point as heat source (heat diffusion maps), and distances from the center point to foreground-background boundaries with fixed angles (star-shaped polygons). However, pixel-wise objectives may lose significant geometric properties of the cell instances, such as shape, curvature, and convexity, which require a collection of pixels to represent. To address this challenge, we present a novel pixel clustering method, called Ceb (for Cell boundaries), to leverage cell boundary features and labels to divide foreground pixels into cell instances. Starting with probability maps generated from semantic segmentation, Ceb first extracts potential foreground-foreground boundaries (i.e., boundary candidates) with a revised Watershed algorithm. For each boundary candidate, a boundary feature representation (called boundary signature) is constructed by sampling pixels from the current foreground-foreground boundary as well as the neighboring background-foreground boundaries. Next, a lightweight boundary classifier is used to predict its binary boundary label based on the corresponding boundary signature. Finally, cell instances are obtained by dividing or merging neighboring regions based on the predicted boundary labels. Extensive experiments on six datasets demonstrate that Ceb outperforms existing pixel clustering methods on semantic segmentation probability maps. Moreover, Ceb achieves highly competitive performance compared to state-of-the-art cell instance segmentation methods. The code is available at: https://github.com/pxliang/Ceb.

Topological structures in image data, such as connected components and loops, play a crucial role in understanding image content (e.g., biomedical objects). Despite remarkable successes of numerous image processing methods that rely on appearance information, these methods often lack sensitivity to topological structures when used in general deep learning (DL) frameworks. In this paper, we introduce a new general approach, called TopoImages (for Topology Images), which computes a new representation of input images by encoding local topology of patches. In TopoImages, we leverage persistent homology (PH) to encode geometric and topological features inherent in image patches. Our main objective is to capture topological information in local patches of an input image into a vectorized form. Specifically, we first compute persistence diagrams (PDs) of the patches, and then vectorize and arrange these PDs into long vectors for pixels of the patches. The resulting multi-channel image-form representation is called a TopoImage. TopoImages offers a new perspective for data analysis. To garner diverse and significant topological features in image data and ensure a more comprehensive and enriched representation, we further generate multiple TopoImages of the input image using various filtration functions, which we call multi-view TopoImages. The multi-view TopoImages are fused with the input image for DL-based classification, with considerable improvement. Our TopoImages approach is highly versatile and can be seamlessly integrated into common DL frameworks. Experiments on three public medical image classification datasets demonstrate noticeably improved accuracy over state-of-the-art methods.

Self-supervised instance discrimination is an effective contrastive pretext task to learn feature representations and address limited medical image annotations. The idea is to make features of transformed versions of the same images similar while forcing all other augmented images’ representations to contrast. However, this instance-based contrastive learning leaves performance on the table by failing to maximize feature affinity between images with similar content while counter-productively pushing their representations apart. Recent improvements on this paradigm (e.g., leveraging multi-modal data, different images in longitudinal studies, spatial correspondences) either relied on additional views or made stringent assumptions about data properties, which can sacrifice generalizability and applicability. To address this challenge, we propose a new self-supervised contrastive learning method that uses unsupervised feature clustering to better select positive and negative image samples. More specifically, we produce pseudo-classes by hierarchically clustering features obtained by an auto-encoder in an unsupervised manner, and prevent destructive interference during contrastive learning by avoiding the selection of negatives from the same pseudo-class. Experiments on 2D skin dermoscopic image segmentation and 3D multi-class whole heart CT segmentation demonstrate that our method outperforms state-of-the-art self-supervised contrastive techniques on these tasks.

Understanding of spatial attributes is central to effective 3D radiology image analysis where crop-based learning is the de facto standard. Given an image patch, its core spatial properties (e.g., position & orientation) provide helpful priors on expected object sizes, appearances, and structures through inherent anatomical consistencies. Spatial correspondences, in particular, can effectively gauge semantic similarities between inter-image regions, while their approximate extraction requires no annotations or overbearing computational costs. However, recent 3D contrastive learning approaches either neglect correspondences or fail to maximally capitalize on them. To this end, we propose an extensible 3D contrastive framework (Spade, for Spa tial De biasing) that leverages extracted correspondences to select more effective positive & negative samples for representation learning. Our method learns both globally invariant and locally equivariant representations with downstream segmentation in mind. We also propose separate selection strategies for global & local scopes that tailor to their respective representational requirements. Compared to recent state-of-the-art approaches, Spade shows notable improvements on three downstream segmentation tasks (CT Abdominal Organ, CT Heart, MR Heart).

In this poster, an approach for best view selection of 3D models is proposed, which is based on the framework that formulates the selection as a problem of evaluating views' discrimination ability. Firstly, different views' features are extracted by unsupervised feature learning. Then classifiers are trained to evaluate each view's discrimination ability. A view with the best classifier has the best discrimination ability, and it is chosen as the best view of the 3D model. At last, experiments show that 3D models of same class have similar best views.