# Transformer-based Detection of Microorganisms on High-Resolution Petri Dish Images

arXiv: https://arxiv.org/abs/2308.09436 · HTML: https://mlsanity.com/paper/2308.09436/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 32 of its 48 references that are in the map.
- First posted on arXiv 18 Aug 2023.

## Builds on (most cited first, 30 of 32)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Microsoft COCO: Common Objects in Context](https://mlsanity.com/paper/1405.0312/) (2014)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [Faster R-CNN: Towards Real-Time Object Detection with Region Proposal Networks](https://mlsanity.com/paper/1506.01497/) (2015)
- [End-to-End Object Detection with Transformers](https://mlsanity.com/paper/2005.12872/) (2020)
- [Mask R-CNN](https://mlsanity.com/paper/1703.06870/) (2017)
- [Layer Normalization](https://mlsanity.com/paper/1607.06450/) (2016)
- [Feature Pyramid Networks for Object Detection](https://mlsanity.com/paper/1612.03144/) (2016)
- [Gaussian Error Linear Units (GELUs)](https://mlsanity.com/paper/1606.08415/) (2016)
- [Deformable DETR: Deformable Transformers for End-to-End Object Detection](https://mlsanity.com/paper/2010.04159/) (2020)
- [SegFormer: Simple and Efficient Design for Semantic Segmentation with Transformers](https://mlsanity.com/paper/2105.15203/) (2021)
- [YOLOv4: Optimal Speed and Accuracy of Object Detection](https://mlsanity.com/paper/2004.10934/) (2020)
- [FCOS: Fully Convolutional One-Stage Object Detection](https://mlsanity.com/paper/1904.01355/) (2019)
- [MMDetection: Open MMLab Detection Toolbox and Benchmark](https://mlsanity.com/paper/1906.07155/) (2019)
- [Cascade R-CNN: Delving into High Quality Object Detection](https://mlsanity.com/paper/1712.00726/) (2017)
- [Path Aggregation Network for Instance Segmentation](https://mlsanity.com/paper/1803.01534/) (2018)
- [Focal Loss for Dense Object Detection](https://mlsanity.com/paper/1708.02002/) (2017)
- [PVT v2: Improved Baselines with Pyramid Vision Transformer](https://mlsanity.com/paper/2106.13797/) (2021)
- [Deformable ConvNets v2: More Deformable, Better Results](https://mlsanity.com/paper/1811.11168/) (2018)
- [CSPNet: A New Backbone that can Enhance Learning Capability of CNN](https://mlsanity.com/paper/1911.11929/) (2019)
- [Bottleneck Transformers for Visual Recognition](https://mlsanity.com/paper/2101.11605/) (2021)
- [VarifocalNet: An IoU-aware Dense Object Detector](https://mlsanity.com/paper/2008.13367/) (2020)
- [TOOD: Task-aligned One-stage Object Detection](https://mlsanity.com/paper/2108.07755/) (2021)
- [AGAR a microbial colony dataset for deep learning detection](https://mlsanity.com/paper/2108.01234/) (2021)
- [Deep Learning to Detect Bacterial Colonies for the Production of Vaccines](https://mlsanity.com/paper/2009.00926/) (2020)
- [Multitask Network for Joint Object Detection, Semantic Segmentation and Human Pose Estimation in Vehicle Occupancy Monitoring](https://mlsanity.com/paper/2205.01515/) (2022)
- [ResFPN: Residual Skip Connections in Multi-Resolution Feature Pyramid Networks for Accurate Dense Pixel Matching](https://mlsanity.com/paper/2006.12235/) (2020)

## Built on by (most cited first, 2 of 2)

- [Boosting Few-Shot Detection with Large Language Models and Layout-to-Image Synthesis](https://mlsanity.com/paper/2410.06841/) (2024)
- [Classifier Ensemble for Efficient Uncertainty Calibration of Deep Neural Networks for Image Classification](https://mlsanity.com/paper/2501.10089/) (2025)

## Abstract (arXiv)

Many medical or pharmaceutical processes have strict guidelines regarding continuous hygiene monitoring. This often involves the labor-intensive task of manually counting microorganisms in Petri dishes by trained personnel. Automation attempts often struggle due to major challenges: significant scaling differences, low separation, low contrast, etc. To address these challenges, we introduce AttnPAFPN, a high-resolution detection pipeline that leverages a novel transformer variation, the efficient-global self-attention mechanism. Our streamlined approach can be easily integrated in almost any multi-scale object detection pipeline. In a comprehensive evaluation on the publicly available AGAR dataset, we demonstrate the superior accuracy of our network over the current state-of-the-art. In order to demonstrate the task-independent performance of our approach, we perform further experiments on COCO and LIVECell datasets.