DeepMIB: User-friendly and open-source software for training of deep learning network for biological image segmentation

Deficiency of the ER-stress-regulator MANF triggers progressive outer hair cell death and hearing loss

(2020) Anni Herranen et al.   Cell Death & Disease

Author Correction: U-Net: deep learning for cell counting, detection, and morphometry

(2019) Thorsten Falk et al.   NATURE METHODS

Deep learning for cellular image analysis

(2019) Erick Moen et al.   NATURE METHODS

ilastik: interactive machine learning for (bio)image analysis

(2019) Stuart Berg et al.   NATURE METHODS

UNI-EM: An Environment for Deep Neural Network-Based Automated Segmentation of Neuronal Electron Microscopic Images

(2019) Hidetoshi Urakubo et al.   Scientific Reports

CellProfiler 3.0: Next-generation image processing for biology

(2018) Claire McQuin et al.   PLOS BIOLOGY

Intelligent Image-Activated Cell Sorting

(2018) Nao Nitta et al.   CELL

Deep learning is combined with massive-scale citizen science to improve large-scale image classification

(2018) Devin P Sullivan et al.   NATURE BIOTECHNOLOGY

CDeep3M—Plug-and-Play cloud-based deep learning for image segmentation

(2018) Matthias G. Haberl et al.   NATURE METHODS

DeepLabCut: markerless pose estimation of user-defined body parts with deep learning

(2018) Alexander Mathis et al.   NATURE NEUROSCIENCE

Content-aware image restoration: pushing the limits of fluorescence microscopy

(2018) Martin Weigert et al.   NATURE METHODS

SegNet: A Deep Convolutional Encoder-Decoder Architecture for Image Segmentation

(2017) Vijay Badrinarayanan et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Advanced Cell Classifier: User-Friendly Machine-Learning-Based Software for Discovering Phenotypes in High-Content Imaging Data

(2017) Filippo Piccinini et al.   Cell Systems

Microscopy Image Browser: A Platform for Segmentation and Analysis of Multidimensional Datasets

(2016) Ilya Belevich et al.   PLOS BIOLOGY

Crowdsourcing the creation of image segmentation algorithms for connectomics

(2015) Ignacio Arganda-Carreras et al.   Frontiers in Neuroanatomy

Connectomic reconstruction of the inner plexiform layer in the mouse retina

(2013) Moritz Helmstaedter et al.   NATURE

Annotated high-throughput microscopy image sets for validation

(2012) Vebjorn Ljosa et al.   NATURE METHODS

Metadata matters: access to image data in the real world

(2010) Melissa Linkert et al.   JOURNAL OF CELL BIOLOGY

An Integrated Micro- and Macroarchitectural Analysis of the Drosophila Brain by Computer-Assisted Serial Section Electron Microscopy

(2010) Albert Cardona et al.   PLOS BIOLOGY