# Towards Generalized Synapse Detection Across Invertebrate Species

arXiv: https://arxiv.org/abs/2509.17041 · HTML: https://mlsanity.com/paper/2509.17041/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 9 of its 38 references that are in the map.
- First posted on arXiv 21 Sep 2025.

## Builds on (most cited first, 9 of 9)

- [SGDR: Stochastic Gradient Descent with Warm Restarts](https://mlsanity.com/paper/1608.03983/) (2016)
- [Objects as Points](https://mlsanity.com/paper/1904.07850/) (2019)
- [Superhuman Accuracy on the SNEMI3D Connectomics Challenge](https://mlsanity.com/paper/1706.00120/) (2017)
- [Synaptic Cleft Segmentation in Non-Isotropic Volume Electron Microscopy of the Complete Drosophila Brain](https://mlsanity.com/paper/1805.02718/) (2018)
- [Synaptic Partner Assignment Using Attentional Voxel Association Networks](https://mlsanity.com/paper/1904.09947/) (2019)
- [Stable deep neural network architectures for mitochondria segmentation on electron microscopy volumes](https://mlsanity.com/paper/2104.03577/) (2021)
- [Fully-Automatic Synapse Prediction and Validation on a Large Data Set](https://mlsanity.com/paper/1604.03075/) (2016)
- [Synaptic partner prediction from point annotations in insect brains](https://mlsanity.com/paper/1806.08205/) (2018)
- [Domain Adaptive Synapse Detection with Weak Point Annotations](https://mlsanity.com/paper/2308.16461/) (2023)

## Abstract (arXiv)

Behavioural differences across organisms, whether healthy or pathological, are closely tied to the structure of their neural circuits. Yet, the fine-scale synaptic changes that give rise to these variations remain poorly understood, in part due to persistent challenges in detecting synapses reliably and at scale. Volume electron microscopy (EM) offers the resolution required to capture synaptic architecture, but automated detection remains difficult due to sparse annotations, morphological variability, and cross-dataset domain shifts. To address this, we make three key contributions. First, we curate a diverse EM benchmark spanning four datasets across two invertebrate species: adult and larval Drosophila melanogaster, and Megaphragma viggianii (micro-WASP). Second, we propose SimpSyn, a single-stage Residual U-Net trained to predict dual-channel spherical masks around pre- and post-synaptic sites, designed to prioritize training and inference speeds and annotation efficiency over architectural complexity. Third, we benchmark SimpSyn against Buhmann et al.'s Synful [1], a state-of-the-art multi-task model that jointly infers synaptic pairs. Despite its simplicity, SimpSyn consistently outperforms Synful in F1-score across all volumes for synaptic site detection. While generalization across datasets remains limited, SimpSyn achieves competitive performance when trained on the combined cohort. Finally, ablations reveal that simple post-processing strategies - such as local peak detection and distance-based filtering - yield strong performance without complex test-time heuristics. Taken together, our results suggest that lightweight models, when aligned with task structure, offer a practical and scalable solution for synapse detection in large-scale connectomic pipelines.