ZAPBench: A Benchmark for Whole-Brain Activity Prediction in Zebrafish

Jan-Matthis Lueckmann, Alexander Immer, Alex Bo-Yuan Chen, Peter H. Li, Mariela D Petkova, Nirmala A Iyer, Luuk Willem Hesselink, Aparna Dev, Gudrun Ihrke, Woohyun Park, Alyson Petruncio, Aubrey Weigel, Wyatt Korff, Florian Engert, Jeff Lichtman, Misha Ahrens, Michal Januszewski, Viren Jain

Keywords: neuroscience, zebrafish, forecasting, benchmark, timeseries, lightsheet microscopy, calcium imaging

TL;DR: ZAPBench evaluates how well different models can predict the activity of over 70,000 neurons in a novel larval zebrafish dataset.

Abstract: 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.

Primary Area: datasets and benchmarks

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Submission Number: 4784