Jeff W. Lichtman

Fuming Yang, Yicong Li, Hanspeter Pfister et al.

Petascale electron microscopy (EM) datasets push storage, transfer, and downstream analysis toward their current limits. We present a vector-quantized variational autoencoder-based (VQ-VAE) compression framework for EM that spans 16x to 1024x and enables pay-as-you-decode usage: top-only decoding for extreme compression, with an optional Transformer prior that predicts bottom tokens (without changing the compression ratio) to restore texture via feature-wise linear modulation (FiLM) and concatenation; we further introduce an ROI-driven workflow that performs selective high-resolution reconstruction from 1024x-compressed latents only where needed.

Xiaofei Hui, Haoxuan Qu, Hossein Rahmani et al.

Analyzing microscopy images to extract biological object properties (e.g., their morphological organization, temporal dynamics, and population density) is fundamental to various biomedical research. Yet conducting this manually is costly and time-consuming. Though deep learning-based approaches have been explored to automate this process, the substantial diversity of microscopy analysis settings in practice (including variations of biological object types, sample processing protocols, imaging equipment, and analysis tasks, etc.) often renders them ineffective. As a result, these approaches typically require extensive adaptation for different settings, which, however, can impose burdens that are often practically unsustainable for laboratories, forcing biomedical researchers to still commonly rely on manual analysis, thereby severely bottlenecking the pace of biomedical research progress. This situation has created a pressing and long-standing need for a reliable and broadly applicable microscopy image analysis tool, yet such a tool is still missing. To address this gap, we present the first ready-to-use microscopy image analysis framework, MicroscopyMatching, that can reliably perform key analysis tasks (including segmentation, tracking, and counting) across diverse microscopy analysis settings. From a fundamentally different perspective, MicroscopyMatching reformulates diverse microscopy image analysis tasks as a unified matching problem, effectively handling this problem by exploiting the robust matching capability from pre-trained latent diffusion models.

Seymour Knowles-Barley, Verena Kaynig, Thouis Ray Jones et al.

Reconstructing a synaptic wiring diagram, or connectome, from electron microscopy (EM) images of brain tissue currently requires many hours of manual annotation or proofreading (Kasthuri and Lichtman, 2010; Lichtman and Sanes, 2008; Seung, 2009). The desire to reconstruct ever larger and more complex networks has pushed the collection of ever larger EM datasets. A cubic millimeter of raw imaging data would take up 1 PB of storage and present an annotation project that would be impractical without relying heavily on automatic segmentation methods. The RhoanaNet image processing pipeline was developed to automatically segment large volumes of EM data and ease the burden of manual proofreading and annotation. Based on (Kaynig et al., 2015), we updated every stage of the software pipeline to provide better throughput performance and higher quality segmentation results. We used state of the art deep learning techniques to generate improved membrane probability maps, and Gala (Nunez-Iglesias et al., 2014) was used to agglomerate 2D segments into 3D objects. We applied the RhoanaNet pipeline to four densely annotated EM datasets, two from mouse cortex, one from cerebellum and one from mouse lateral geniculate nucleus (LGN). All training and test data is made available for benchmark comparisons. The best segmentation results obtained gave $V^\text{Info}_\text{F-score}$ scores of 0.9054 and 09182 for the cortex datasets, 0.9438 for LGN, and 0.9150 for Cerebellum. The RhoanaNet pipeline is open source software. All source code, training data, test data, and annotations for all four benchmark datasets are available at www.rhoana.org.

Jan-Matthis Lueckmann, Alexander Immer, Alex Bo-Yuan Chen et al.

Data-driven benchmarks have led to significant progress in key scientific modeling domains including weather and structural biology. Here, we introduce the Zebrafish Activity Prediction Benchmark (ZAPBench) to measure progress on the problem of predicting cellular-resolution neural activity throughout an entire vertebrate brain. The benchmark is based on a novel dataset containing 4d light-sheet microscopy recordings of over 70,000 neurons in a larval zebrafish brain, along with motion stabilized and voxel-level cell segmentations of these data that facilitate development of a variety of forecasting methods. Initial results from a selection of time series and volumetric video modeling approaches achieve better performance than naive baseline methods, but also show room for further improvement. The specific brain used in the activity recording is also undergoing synaptic-level anatomical mapping, which will enable future integration of detailed structural information into forecasting methods.

Alexander Immer, Jan-Matthis Lueckmann, Alex Bo-Yuan Chen et al.

Large-scale neuronal activity recordings with fluorescent calcium indicators are increasingly common, yielding high-resolution 2D or 3D videos. Traditional analysis pipelines reduce this data to 1D traces by segmenting regions of interest, leading to inevitable information loss. Inspired by the success of deep learning on minimally processed data in other domains, we investigate the potential of forecasting neuronal activity directly from volumetric videos. To capture long-range dependencies in high-resolution volumetric whole-brain recordings, we design a model with large receptive fields, which allow it to integrate information from distant regions within the brain. We explore the effects of pre-training and perform extensive model selection, analyzing spatio-temporal trade-offs for generating accurate forecasts. Our model outperforms trace-based forecasting approaches on ZAPBench, a recently proposed benchmark on whole-brain activity prediction in zebrafish, demonstrating the advantages of preserving the spatial structure of neuronal activity.