ilastik: interactive machine learning for (bio)image analysis

Quanti.us: a tool for rapid, flexible, crowd-based annotation of images

(2018) Alex J. Hughes et al.   NATURE METHODS

Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb

(2018) Carsten Wolff et al.   eLife

TANGO1 builds a machine for collagen export by recruiting and spatially organizing COPII, tethers and membranes

(2018) Ishier Raote et al.   eLife

NeuroMorph: A Software Toolset for 3D Analysis of Neurite Morphology and Connectivity

(2018) Anne Jorstad et al.   Frontiers in Neuroanatomy

SuRVoS: Super-Region Volume Segmentation workbench

(2017) Imanol Luengo et al.   JOURNAL OF STRUCTURAL BIOLOGY

A deep learning and novelty detection framework for rapid phenotyping in high-content screening

(2017) Christoph Sommer et al.   MOLECULAR BIOLOGY OF THE CELL

Multicut brings automated neurite segmentation closer to human performance

(2017) Thorsten Beier et al.   NATURE METHODS

Machine Learning for Medical Imaging

(2017) Bradley J. Erickson et al.   RADIOGRAPHICS

Collaborative analysis of multi-gigapixel imaging data using Cytomine

(2016) Raphaël Marée et al.   BIOINFORMATICS

Increased spatiotemporal resolution reveals highly dynamic dense tubular matrices in the peripheral ER

(2016) J. Nixon-Abell et al.   SCIENCE

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

(2016) Ilya Belevich et al.   PLOS BIOLOGY

Ultrastructural analysis of adult mouse neocortex comparing aldehyde perfusion with cryo fixation

(2015) Natalya Korogod et al.   eLife

Spatial constraints control cell proliferation in tissues

(2014) S. J. Streichan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Correlative In Vivo 2 Photon and Focused Ion Beam Scanning Electron Microscopy of Cortical Neurons

(2013) Bohumil Maco et al.   PLoS One

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

(2012) Johannes Schindelin et al.   NATURE METHODS

Metadata matters: access to image data in the real world

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

Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes

(2010) Beate Neumann et al.   NATURE

Auto-Context and Its Application to High-Level Vision Tasks and 3D Brain Image Segmentation

(2009) Zhuowen Tu et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Supervised learning with decision tree-based methods in computational and systems biology

(2009) Pierre Geurts et al.   Molecular BioSystems