45 citations · 52 across the 13 of their papers we have counts for
14 papers
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…
Budgeted Broadcast: An Activity-Dependent Pruning Rule for Neural Network Efficiency
Yaron Meirovitch, Fuming Yang, Jeff Lichtman +1
Most pruning methods remove parameters ranked by impact on loss (e.g., magnitude or gradient). We propose Budgeted Broadcast (BB), which gives each unit a local traffic budget (the…
Sparse Graph Reconstruction and Seriation for Large-Scale Image Stacks
Fuming Yang, Yaron Meirovitch, Jeff W. Lichtman
We study recovering a 1D order from a noisy, locally sampled pairwise comparison matrix under a tight query budget. We recast the task as reconstructing a sparse, noisy line graph…
ZAPBench: A Benchmark for Whole-Brain Activity Prediction in Zebrafish
Jan-Matthis Lueckmann, Alexander Immer, Alex Bo-Yuan Chen +15
Data-driven benchmarks have led to significant progress in key scientific modeling domains including weather and structural biology. Here, we introduce the Zebrafish Activity Predi…
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…
Registering large volume serial-section electron microscopy image sets for neural circuit reconstruction using FFT signal whitening
Arthur W. Wetzel, Jennifer Bakal, Markus Dittrich +3
The detailed reconstruction of neural anatomy for connectomics studies requires a combination of resolution and large three-dimensional data capture provided by serial section elec…
Efficiency of Cathodoluminescence Emission by Nitrogen-Vacancy Color Centers in Nanodiamond
Huiliang Zhang, David R. Glenn, Richard Schalek +2
Correlated electron microscopy and cathodoluminescence (CL) imaging using functionalized nanoparticles is a promising nanoscale probe of biological structure and function. Nanodiam…
Automatic Annotation of Axoplasmic Reticula in Pursuit of Connectomes
Ayushi Sinha, William Gray Roncal, Narayanan Kasthuri +8
In this paper, we present a new pipeline which automatically identifies and annotates axoplasmic reticula, which are small subcellular structures present only in axons. We run our…
Silicon-Vacancy Color Centers in Nanodiamonds: Cathodoluminescence Imaging Marker in the Near Infrared
Huiliang Zhang, Igor Aharonovich, David R. Glenn +5
We demonstrate that nanodiamonds fabricated to incorporate silicon-vacancy (Si-V) color centers provide bright, spectrally narrow, and stable cathodoluminescence (CL) in the near-i…
Multi-color correlative light and electron microscopy using nanoparticle cathodoluminescence
David R. Glenn, Huiliang Zhang, Narayanan Kasthuri +6
Correlative light and electron microscopy promises to combine molecular specificity with nanoscale imaging resolution. However, there are substantial technical challenges including…