# Deep-learning in the bioimaging wild: Handling ambiguous data with deepflash2

arXiv: https://arxiv.org/abs/2111.06693 · HTML: https://mlsanity.com/paper/2111.06693/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 23 of its 56 references that are in the map.
- First posted on arXiv 12 Nov 2021.

## Builds on (most cited first, 23 of 23)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [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)
- [Mask R-CNN](https://mlsanity.com/paper/1703.06870/) (2017)
- [EfficientNet: Rethinking Model Scaling for Convolutional Neural Networks](https://mlsanity.com/paper/1905.11946/) (2019)
- ["Why Should I Trust You?": Explaining the Predictions of Any Classifier](https://mlsanity.com/paper/1602.04938/) (2016)
- [Dropout as a Bayesian Approximation: Representing Model Uncertainty in Deep Learning](https://mlsanity.com/paper/1506.02142/) (2015)
- [Simple and Scalable Predictive Uncertainty Estimation using Deep Ensembles](https://mlsanity.com/paper/1612.01474/) (2016)
- [Delving Deep into Rectifiers: Surpassing Human-Level Performance on ImageNet Classification](https://mlsanity.com/paper/1502.01852/) (2015)
- [Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation](https://mlsanity.com/paper/1802.02611/) (2018)
- [UNet++: A Nested U-Net Architecture for Medical Image Segmentation](https://mlsanity.com/paper/1807.10165/) (2018)
- [Deep Bayesian Active Learning with Image Data](https://mlsanity.com/paper/1703.02910/) (2017)
- [Albumentations: fast and flexible image augmentations](https://mlsanity.com/paper/1809.06839/) (2018)
- [ResNeSt: Split-Attention Networks](https://mlsanity.com/paper/2004.08955/) (2020)
- [A Probabilistic U-Net for Segmentation of Ambiguous Images](https://mlsanity.com/paper/1806.05034/) (2018)
- [Aleatoric uncertainty estimation with test-time augmentation for medical image segmentation with convolutional neural networks](https://mlsanity.com/paper/1807.07356/) (2018)
- [Tversky loss function for image segmentation using 3D fully convolutional deep networks](https://mlsanity.com/paper/1706.05721/) (2017)
- [A disciplined approach to neural network hyper-parameters: Part 1 -- learning rate, batch size, momentum, and weight decay](https://mlsanity.com/paper/1803.09820/) (2018)
- [Cell Detection with Star-convex Polygons](https://mlsanity.com/paper/1806.03535/) (2018)
- [fastai: A Layered API for Deep Learning](https://mlsanity.com/paper/2002.04688/) (2020)
- [The Importance of Skip Connections in Biomedical Image Segmentation](https://mlsanity.com/paper/1608.04117/) (2016)

## Abstract (arXiv)

We present deepflash2, a deep learning solution that facilitates the objective and reliable segmentation of ambiguous bioimages through multi-expert annotations and integrated quality assurance. Thereby, deepflash2 addresses typical challenges that arise during training, evaluation, and application of deep learning models in bioimaging. The tool is embedded in an easy-to-use graphical user interface and offers best-in-class predictive performance for semantic and instance segmentation under economical usage of computational resources.