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MicroscopyMatching: Towards a Ready-to-use Framework for Microscopy Image Analysis in Diverse Conditions
Xiaofei Hui, Haoxuan Qu, Hossein Rahmani +3
Analyzing microscopy images to extract biological object properties (e.g., their morphological organization, temporal dynamics, and population density) is fundamental to various bi…
Towards 1000-fold Electron Microscopy Image Compression for Connectomics via VQ-VAE with Transformer Prior
Fuming Yang, Yicong Li, Hanspeter Pfister +2
Petascale electron microscopy (EM) datasets push storage, transfer, and downstream analysis toward their current limits. We present a vector-quantized variational autoencoder-based…
Forecasting Whole-Brain Neuronal Activity from Volumetric Video
Alexander Immer, Jan-Matthis Lueckmann, Alex Bo-Yuan Chen +14
Large-scale neuronal activity recordings with fluorescent calcium indicators are increasingly common, yielding high-resolution 2D or 3D videos. Traditional analysis pipelines reduc…
Frenet-Serret Frame-based Decomposition for Part Segmentation of 3D Curvilinear Structures
Leslie Gu, Jason Ken Adhinarta, Mikhail Bessmeltsev +7
Accurately segmenting 3D curvilinear structures in medical imaging remains challenging due to their complex geometry and the scarcity of diverse, large-scale datasets for algorithm…
TriSAM: Tri-Plane SAM for zero-shot cortical blood vessel segmentation in VEM images
Jia Wan, Wanhua Li, Jason Ken Adhinarta +6
While imaging techniques at macro and mesoscales have garnered substantial attention and resources, microscale Volume Electron Microscopy (vEM) imaging, capable of revealing intric…
AxonEM Dataset: 3D Axon Instance Segmentation of Brain Cortical Regions
Donglai Wei, Kisuk Lee, Hanyu Li +13
Electron microscopy (EM) enables the reconstruction of neural circuits at the level of individual synapses, which has been transformative for scientific discoveries. However, due t…