# Implicit neural representations for larval zebrafish brain microscopy: a reproducible benchmark on the MapZebrain atlas

arXiv: https://arxiv.org/abs/2603.26811 · HTML: https://mlsanity.com/paper/2603.26811/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 10 of its 16 references that are in the map.
- First posted on arXiv 26 Mar 2026.

## Builds on (most cited first, 10 of 10)

- [Instant Neural Graphics Primitives with a Multiresolution Hash Encoding](https://mlsanity.com/paper/2201.05989/) (2022)
- [DeepSDF: Learning Continuous Signed Distance Functions for Shape Representation](https://mlsanity.com/paper/1901.05103/) (2019)
- [Implicit Neural Representations with Periodic Activation Functions](https://mlsanity.com/paper/2006.09661/) (2020)
- [Fourier Features Let Networks Learn High Frequency Functions in Low Dimensional Domains](https://mlsanity.com/paper/2006.10739/) (2020)
- [Occupancy Networks: Learning 3D Reconstruction in Function Space](https://mlsanity.com/paper/1812.03828/) (2018)
- [On the Spectral Bias of Neural Networks](https://mlsanity.com/paper/1806.08734/) (2018)
- [Learning Continuous Image Representation with Local Implicit Image Function](https://mlsanity.com/paper/2012.09161/) (2020)
- [Neural Fields in Visual Computing and Beyond](https://mlsanity.com/paper/2111.11426/) (2021)
- [Implicit Neural Representations for Image Compression](https://mlsanity.com/paper/2112.04267/) (2021)
- [VoxGRAF: Fast 3D-Aware Image Synthesis with Sparse Voxel Grids](https://mlsanity.com/paper/2206.07695/) (2022)

## Abstract (arXiv)

Implicit neural representations (INRs) offer continuous coordinate-based encodings for atlas registration, cross-modality resampling, sparse-view completion, and compact sharing of neuroanatomical data. Yet reproducible evaluation is lacking for high-resolution larval zebrafish microscopy, where preserving neuropil boundaries and fine neuronal processes is critical. We present a reproducible INR benchmark for the MapZebrain larval zebrafish brain atlas. Using a unified, seed-controlled protocol, we compare SIREN, Fourier features, Haar positional encoding, and a multi-resolution grid on 950 grayscale microscopy images, including atlas slices and single-neuron projections. Images are normalized with per-image (1,99) percentiles estimated from 10% of pixels in non-held-out columns, and spatial generalization is tested with a deterministic 40% column-wise hold-out along the X-axis. Haar and Fourier achieve the strongest macro-averaged reconstruction fidelity on held-out columns (about 26 dB), while the grid is moderately behind. SIREN performs worse in macro averages but remains competitive on area-weighted micro averages in the all-in-one regime. SSIM and edge-focused error further show that Haar and Fourier preserve boundaries more accurately. These results indicate that explicit spectral and multiscale encodings better capture high-frequency neuroanatomical detail than smoother-bias alternatives. For MapZebrain workflows, Haar and Fourier are best suited to boundary-sensitive tasks such as atlas registration, label transfer, and morphology-preserving sharing, while SIREN remains a lightweight baseline for background modelling or denoising.