Antonis Vamvakeros

Ronan Docherty, Isaac Squires, Antonis Vamvakeros et al.

Segmentation is the assigning of a semantic class to every pixel in an image and is a prerequisite for various statistical analysis tasks in materials science, like phase quantification, physics simulations or morphological characterization. The wide range of length scales, imaging techniques and materials studied in materials science means any segmentation algorithm must generalise to unseen data and support abstract, user-defined semantic classes. Trainable segmentation is a popular interactive segmentation paradigm where a classifier is trained to map from image features to user drawn labels. SAMBA is a trainable segmentation tool that uses Meta's Segment Anything Model (SAM) for fast, high-quality label suggestions and a random forest classifier for robust, generalizable segmentations. It is accessible in the browser (https://www.sambasegment.com/) without the need to download any external dependencies. The segmentation backend is run in the cloud, so does not require the user to have powerful hardware.

Ronan Docherty, Antonis Vamvakeros, Samuel J. Cooper

The features of self-supervised vision transformers (ViTs) contain strong semantic and positional information relevant to downstream tasks like object localization and segmentation. Recent works combine these features with traditional methods like clustering, graph partitioning or region correlations to achieve impressive baselines without finetuning or training additional networks. We leverage upsampled features from ViT networks (e.g DINOv2) in two workflows: in a clustering based approach for object localization and segmentation, and paired with standard classifiers in weakly supervised materials segmentation. Both show strong performance on benchmarks, especially in weakly supervised segmentation where the ViT features capture complex relationships inaccessible to classical approaches. We expect the flexibility and generalizability of these features will both speed up and strengthen materials characterization, from segmentation to property-prediction.

Ronan Docherty, Antonis Vamvakeros, Samuel J. Cooper

Feature foundation models - usually vision transformers - offer rich semantic descriptors of images, useful for downstream tasks such as (interactive) segmentation and object detection. For computational efficiency these descriptors are often patch-based, and so struggle to represent the fine features often present in micrographs; they also struggle with the large image sizes present in materials and biological image analysis. In this work, we train a convolutional neural network to upsample low-resolution (i.e, large patch size) foundation model features with reference to the input image. We apply this upsampler network (without any further training) to efficiently featurise and then segment a variety of microscopy images, including plant cells, a lithium-ion battery cathode and organic crystals. The richness of these upsampled features admits separation of hard to segment phases, like hairline cracks. We demonstrate that interactive segmentation with these deep features produces high-quality segmentations far faster and with far fewer labels than training or finetuning a more traditional convolutional network.