# Implicit neural image field for biological microscopy image compression

**Authors:** Gaole Dai, Rongyu Zhang, Qingpo Wuwu, Cheng-Ching Tseng, Yu Zhou, Shaokang Wang, Siyuan Qian, Ming Lu, Ali Ata Tuz, Matthias Gunzer, Tiejun Huang, Jianxu Chen, Shanghang Zhang

PMC · DOI: 10.1038/s43588-025-00889-4 · Nature Computational Science · 2025-10-10

## TL;DR

This paper introduces a new AI-based method for compressing large biological microscopy images while preserving important details for scientific analysis.

## Contribution

The novel contribution is an adaptive compression workflow using implicit neural representation for bioimages.

## Key findings

- The workflow achieves high, controllable compression ratios on real-world microscopy images.
- It preserves critical details necessary for downstream scientific analysis.
- The method supports arbitrary pixel-wise decompression and varying image dimensionalities.

## Abstract

The rapid pace of innovation in biological microscopy has produced increasingly large images, putting pressure on data storage and impeding efficient data sharing, management and visualization. This trend necessitates new, efficient compression solutions, as traditional coder–decoder methods often struggle with the diversity of bioimages, leading to suboptimal results. Here we show an adaptive compression workflow based on implicit neural representation that addresses these challenges. Our approach enables application-specific compression, supports images of varying dimensionality and allows arbitrary pixel-wise decompression. On a wide range of real-world microscopy images, we demonstrate that our workflow achieves high, controllable compression ratios while preserving the critical details necessary for downstream scientific analysis.

This study presents a flexible AI-based method for compressing microscopy images, achieving high compression while preserving details critical for analysis, with support for task-specific optimization and arbitrary-resolution decompression.

## Full-text entities

- **Genes:** Pphln1 (periphilin 1) [NCBI Gene 223828] {aka CR, HSPC206, HSPC232}, CMPK1 (cytidine/uridine monophosphate kinase 1) [NCBI Gene 51727] {aka CK, CMK, CMPK, UMK, UMP-CMPK, UMPK}, CETN2 [NCBI Gene 660873], srn (siren) [NCBI Gene 20812], PDPN (podoplanin) [NCBI Gene 10630] {aka AGGRUS, D2-40, GP36, GP40, Gp38, HT1A-1}, S100A4 (S100 calcium binding protein A4) [NCBI Gene 6275] {aka 18A2, 42A, CAPL, FSP1, MTS1, P9KA}
- **Diseases:** hiPS (MESH:D020295), cancer (MESH:D009369), TNBC (MESH:D064726), breast tumor (MESH:D001943)
- **Chemicals:** 4',6-diamidino-2-phenylindole (MESH:C007293), CODEC (-), thymine (MESH:D013941), adenine (MESH:D000225)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], Tribolium castaneum (red flour beetle, species) [taxon 7070], Homo sapiens (human, species) [taxon 9606]
- **Cell lines:** hiPS — Gallus gallus (Chicken), Induced pluripotent stem cell (CVCL_YE48), -11 — Homo sapiens (Human), Transformed cell line (CVCL_C1JD), WTC-11 — Homo sapiens (Human), Induced pluripotent stem cell (CVCL_Y803)

## Full text

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## Figures

8 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12638249/full.md

## References

23 references — full list in the complete paper: https://tomesphere.com/paper/PMC12638249/full.md

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Source: https://tomesphere.com/paper/PMC12638249