4.8 Article

Democratising deep learning for microscopy with ZeroCostDL4Mic

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

EM-stellar: benchmarking deep learning for electron microscopy image segmentation

Afshin Khadangi et al.

Summary: This research introduces a platform called EM-stellar for benchmarking the performance of various state-of-the-art DL methods on user-provided datasets. The study finds that the performance of any DL method depends on the properties of the images being segmented, and no single DL method consistently performs across all performance evaluation metrics.

BIOINFORMATICS (2021)

Article Biochemical Research Methods

Cellpose: a generalist algorithm for cellular segmentation

Carsen Stringer et al.

Summary: Cellpose is a generalist, deep learning-based segmentation method that can precisely segment cells from various types of images without requiring retraining or parameter adjustments. It was trained on a highly diverse image dataset and supports a three-dimensional extension. Software has been developed to support community contributions to the training data.

NATURE METHODS (2021)

Article Biochemical Research Methods

DeepCell Kiosk: scaling deep learning-enabled cellular image analysis with Kubernetes

Dylan Bannon et al.

Summary: Deep learning is changing the analysis of biological images, and the DeepCell Kiosk is a cloud-native software that can dynamically scale deep learning workflows for large imaging datasets. This software allows for efficient identification of cell nuclei in large-scale images at a relatively low cost, demonstrating scalability and affordability.

NATURE METHODS (2021)

Article Biochemical Research Methods

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

Ilya Belevich et al.

Summary: DeepMIB is a software package for training convolutional neural networks for segmentation of multidimensional microscopy datasets. It is capable of handling 2D and 3D datasets with isotropic and anisotropic voxels, and is distributed as open-source Matlab code and standalone application for different operating systems. It is a user-friendly tool that does not require programming knowledge, suitable for users interested in applying deep learning to image segmentation workflows.

PLOS COMPUTATIONAL BIOLOGY (2021)

Review Biochemical Research Methods

About samples, giving examples: Optimized Single Molecule Localization Microscopy

Angelique Jimenez et al.

METHODS (2020)

Review Physics, Applied

Between life and death: strategies to reduce phototoxicity in super-resolution microscopy

Kalina L. Tosheva et al.

JOURNAL OF PHYSICS D-APPLIED PHYSICS (2020)

Article Chemistry, Multidisciplinary

Fluctuation-Based Super-Resolution Traction Force Microscopy

Aki Stubb et al.

NANO LETTERS (2020)

Review Biochemical Research Methods

Deep learning in single-molecule microscopy: fundamentals, caveats, and recent developments [Invited]

Leonhard Mockl et al.

BIOMEDICAL OPTICS EXPRESS (2020)

Meeting Abstract Biochemistry & Molecular Biology

Deep Learning-Based Point-Scanning Super-Resolution Imaging

Uri Manor et al.

FASEB JOURNAL (2020)

Article Multidisciplinary Sciences

On instabilities of deep learning in image reconstruction and the potential costs of AI

Vegard Antun et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Multidisciplinary Sciences

Deep learning enables structured illumination microscopy with low light levels and enhanced speed

Luhong Jin et al.

NATURE COMMUNICATIONS (2020)

Article Biochemistry & Molecular Biology

nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer

Reka Hollandi et al.

CELL SYSTEMS (2020)

Article Cell Biology

The cell biologist's guide to super-resolution microscopy

Guillaume Jacquemet et al.

JOURNAL OF CELL SCIENCE (2020)

Article Cell Biology

AnnotatorJ: an ImageJ plugin to ease hand annotation of cellular compartments

Reka Hollandi et al.

MOLECULAR BIOLOGY OF THE CELL (2020)

Article Multidisciplinary Sciences

Neuronal activity remodels the F-actin based submembrane lattice in dendrites but not axons of hippocampal neurons

Flavie Lavoie-Cardinal et al.

SCIENTIFIC REPORTS (2020)

Review Multidisciplinary Sciences

Array programming with NumPy

Charles R. Harris et al.

NATURE (2020)

Article Biochemical Research Methods

Practical fluorescence reconstruction microscopy for large samples and low-magnification imaging

Julienne LaChance et al.

PLOS COMPUTATIONAL BIOLOGY (2020)

Review Physics, Applied

NanoJ: a high-performance open-source super-resolution microscopy toolbox

Romain F. Laine et al.

JOURNAL OF PHYSICS D-APPLIED PHYSICS (2019)

Article Biochemistry & Molecular Biology

PlotsOfDataA web app for visualizing data together with their summaries

Marten Postma et al.

PLOS BIOLOGY (2019)

Article Biochemical Research Methods

Biomedical image augmentation using Augmentor

Marcus D. Bloice et al.

BIOINFORMATICS (2019)

Review Biochemical Research Methods

Deep learning for cellular image analysis

Erick Moen et al.

NATURE METHODS (2019)

Review Biochemistry & Molecular Biology

Artificial intelligence for microscopy: what you should know

Lucas von Chamier et al.

BIOCHEMICAL SOCIETY TRANSACTIONS (2019)

Article Biochemical Research Methods

Applications, promises, and pitfalls of deep learning for fluorescence image reconstruction

Chinmay Belthangady et al.

NATURE METHODS (2019)

Article Biochemical Research Methods

ilastik: interactive machine learning for (bio) image analysis

Stuart Berg et al.

NATURE METHODS (2019)

Letter Biochemical Research Methods

ImJoy: an open-source computational platform for the deep learning era

Wei Ouyang et al.

NATURE METHODS (2019)

Article Biochemical Research Methods

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

Thorsten Falk et al.

NATURE METHODS (2019)

Article Multidisciplinary Sciences

Ultrastructure of the axonal periodic scaffold reveals a braid-like organization of actin rings

Stephane Vassilopoulos et al.

NATURE COMMUNICATIONS (2019)

Editorial Material Biochemical Research Methods

Hessian structured illumination microscopy

Rita Strack

NATURE METHODS (2018)

Article Biochemical Research Methods

Quantitative mapping and minimization of super-resolution optical imaging artifacts

Sian Culley et al.

NATURE METHODS (2018)

Article Biochemistry & Molecular Biology

CellProfiler 3.0: Next-generation image processing for biology

Claire McQuin et al.

PLOS BIOLOGY (2018)

Article Anatomy & Morphology

Molecular imaging with neural training of identification algorithm (neural network localization identification)

A. J. Nelson et al.

MICROSCOPY RESEARCH AND TECHNIQUE (2018)

Article Biochemical Research Methods

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

Matthias G. Haberl et al.

NATURE METHODS (2018)

Article Biochemical Research Methods

Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy

Chawin Ounkomol et al.

NATURE METHODS (2018)

Article Biochemical Research Methods

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

Martin Weigert et al.

NATURE METHODS (2018)

Article Computer Science, Information Systems

Performance Analysis of Google Colaboratory as a Tool for Accelerating Deep Learning Applications

Tiago Carneiro et al.

IEEE ACCESS (2018)

Article Cell Biology

FiloQuant reveals increased filopodia density during breast cancer progression

Guillaume Jacquemet et al.

JOURNAL OF CELL BIOLOGY (2017)

Article Computer Science, Artificial Intelligence

A survey on deep learning in medical image analysis

Geert Litjens et al.

MEDICAL IMAGE ANALYSIS (2017)

Article Biochemical Research Methods

TrackMate: An open and extensible platform for single-particle tracking

Jean-Yves Tinevez et al.

METHODS (2017)

Article Multidisciplinary Sciences

Classification of breast cancer histology images using Convolutional Neural Networks

Teresa Araujo et al.

PLOS ONE (2017)

Article Biochemical Research Methods

ImageJ2: ImageJ for the next generation of scientific image data

Curtis T. Rueden et al.

BMC BIOINFORMATICS (2017)

Proceedings Paper Computer Science, Artificial Intelligence

Image-to-Image Translation with Conditional Adversarial Networks

Phillip Isola et al.

30TH IEEE CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION (CVPR 2017) (2017)

Article Biochemical Research Methods

High-density three-dimensional localization microscopy across large volumes

Wesley R. Legant et al.

NATURE METHODS (2016)

Article Multidisciplinary Sciences

L-type calcium channels regulate filopodia stability and cancer cell invasion downstream of integrin signalling

Guillaume Jacquemet et al.

NATURE COMMUNICATIONS (2016)

Article Multidisciplinary Sciences

Fast live-cell conventional fluorophore nanoscopy with ImageJ through super-resolution radial fluctuations

Nils Gustafsson et al.

NATURE COMMUNICATIONS (2016)

Article Biochemical Research Methods

Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments

David A. Van Valen et al.

PLOS COMPUTATIONAL BIOLOGY (2016)

Review Multidisciplinary Sciences

Deep learning

Yann LeCun et al.

NATURE (2015)

Article Biochemical Research Methods

SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data

Florian Levet et al.

NATURE METHODS (2015)

Article Anatomy & Morphology

Crowdsourcing the creation of image segmentation algorithms for connectomics

Ignacio Arganda-Carreras et al.

FRONTIERS IN NEUROANATOMY (2015)

Article Biochemical Research Methods

Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT

Ralf Jungmann et al.

NATURE METHODS (2014)

Article Biochemical Research Methods

Fiji: an open-source platform for biological-image analysis

Johannes Schindelin et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

Probing protein heterogeneity in the plasma membrane using PALM and pair correlation analysis

Prabuddha Sengupta et al.

NATURE METHODS (2011)

Article Optics

Sample drift correction in 3D fluorescence photoactivation localization microscopy

Michael J. Mlodzianoski et al.

OPTICS EXPRESS (2011)

Article Computer Science, Artificial Intelligence

A Survey on Transfer Learning

Sinno Jialin Pan et al.

IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING (2010)

Article Biochemical Research Methods

PALM imaging and cluster analysis of protein heterogeneity at the cell surface

Dylan M. Owen et al.

JOURNAL OF BIOPHOTONICS (2010)

Article Chemistry, Multidisciplinary

Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes

Mike Heilemann et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2008)

Article Computer Science, Artificial Intelligence

Image quality assessment: From error visibility to structural similarity

Z Wang et al.

IEEE TRANSACTIONS ON IMAGE PROCESSING (2004)