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Michal Januszewski

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2 papers

2 author rows

ICLR Conference 2025 Conference Paper

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

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.

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NeurIPS Conference 2016 Conference Paper

Combinatorial Energy Learning for Image Segmentation

Jeremy Maitin-Shepard
Viren Jain
Michal Januszewski
Peter Li
Pieter Abbeel

We introduce a new machine learning approach for image segmentation that uses a neural network to model the conditional energy of a segmentation given an image. Our approach, combinatorial energy learning for image segmentation (CELIS) places a particular emphasis on modeling the inherent combinatorial nature of dense image segmentation problems. We propose efficient algorithms for learning deep neural networks to model the energy function, and for local optimization of this energy in the space of supervoxel agglomerations. We extensively evaluate our method on a publicly available 3-D microscopy dataset with 25 billion voxels of ground truth data. On an 11 billion voxel test set, we find that our method improves volumetric reconstruction accuracy by more than 20% as compared to two state-of-the-art baseline methods: graph-based segmentation of the output of a 3-D convolutional neural network trained to predict boundaries, as well as a random forest classifier trained to agglomerate supervoxels that were generated by a 3-D convolutional neural network.

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