Unknown (59)#

2022 MIC Workshop on Bioimage processing with Python#

[‘Guillaume Witz’]

Licensed UNKNOWN

Tags: Python, Bioimage Analysis

Content type: Notebook

guiwitz/MICPy_Workshop_2022

AI4Life teams up with Galaxy Training Network (GTN) to enhance training resources#

[‘Caterina Fuster-Barceló’]

Licensed UNKNOWN

Tags: Artificial Intelligence, Workflow Engine, Bio-Image Analysis

Content type: Documentation

https://ai4life.eurobioimaging.eu/ai4life-teams-up-with-galaxy-training-network-gtn-to-enhance-training-resources/

Analysis of High-Throughput Microscopy Image Data#

[‘Kota Miura’, ‘Christoph Schiklenk’, ‘Clemens Lakner’, ‘Christian Tischer’, ‘Aliaksandr Halavatyi’]

Published 2014

Licensed UNKNOWN

miura/HTManalysisCourse

Bio Image Analysis#

[‘Christian Tischer’]

Licensed UNKNOWN

Tags: Bioimage Analysis

Content type: Slide

tischi/presentation-image-analysis

BioEngine#

[‘Jeremy Metz’, ‘Beatriz Serrano-Solano’, ‘Wei Ouyang’]

Licensed UNKNOWN

BioEnging is a cloud infrastructure to run BioImage model zoo based workflows in the cloud.

Tags: Artificial Intelligence, Workflow Engine

Content type: Publication

https://ai4life.eurobioimaging.eu/announcing-bioengine/

Bioimage Model Zoo#

Licensed UNKNOWN

Tags: Bioimage Analysis, Artificial Intelligence

Content type: Collection

https://bioimage.io/

Building a Bioimage Analysis Workflow using Deep Learning#

[‘Estibaliz Gómez-de-Mariscal']

Licensed UNKNOWN

Tags: Artificial Intelligence, Bioimage Analysis

Content type: Slide

esgomezm/NEUBIAS_chapter_DL_2020

CARE/Stardist tutorials for EMBO Practical Course — Computational optical biology 2022#

[‘Martin Weigert’]

Licensed UNKNOWN

Tags: Python, Artificial Intelligence, Bioimage Analysis

Content type: Notebook

maweigert/embo_2022

CSBDeep and StarDist @ I2K 2020#

[‘Martin Weigert’, ‘Uwe Schmidt’]

Licensed UNKNOWN

Tags: Python, Artificial Intelligence, Bioimage Analysis

Content type: Notebook

maweigert/stardist-i2k

Cell Tracking Challenge - 2D Datasets#

Licensed UNKNOWN

Tags: Bioimage Analysis

Content type: Collection, Data

http://celltrackingchallenge.net/2d-datasets/

Cell Tracking Challenge - 3D Datasets#

Licensed UNKNOWN

Tags: Bioimage Analysis

Content type: Collection, Data

http://celltrackingchallenge.net/3d-datasets/

CellProfiler Introduction#

[‘Anna Klemm’]

Licensed UNKNOWN

Tags: Neubias, Cellprofiler, Bioimage Analysis

Content type: Slide

ahklemm/CellProfiler_Introduction

CellProfiler Practical NeuBIAS Lisbon 2017#

[‘Carolina Wählby’, ‘Maxime Bombrun’, ‘Christian Tischer’]

Licensed UNKNOWN

Tags: Neubias, Cellprofiler, Bioimage Analysis

Content type: Tutorial

tischi/cellprofiler-practical-NeuBIAS-Lisbon-2017

Chris Halvin YouTube channel#

Licensed UNKNOWN

Tags: Napari, Python, Bioimage Analysis

Content type: Collection, Video

https://www.youtube.com/@chrishavlin

https://www.youtube.com/playlist?list=PLqbhAmYZU5KxuAcnNBIxyBkivUEiKswq1

Course on Deep Learning for imaging using PyTorch#

[‘Guillaume Witz’]

Licensed UNKNOWN

Tags: Python, Bioimage Analysis, Artificial Intelligence

Content type: Notebook

guiwitz/DLImaging

DEEP NAPARI : Napari as a tool for deep learning project management#

[‘Herearii Metuarea’, ‘David Rousseau’, ‘Pejman Rasti’, ‘Valentin Gilet’]

Licensed UNKNOWN

Tags: Artificial Intelligence, Bioimage Analysis

Content type: Notebook

hereariim/DEEP-NAPARI

DL@MBL 2021 Exercises#

[‘Jan Funke’, ‘Constantin Pape’, ‘Morgan Schwartz’, ‘Xiaoyan’]

Licensed UNKNOWN

Tags: Artificial Intelligence, Bioimage Analysis

Content type: Slide, Notebook

JLrumberger/DL-MBL-2021

Dask Course#

[‘Guillaume Witz’]

Licensed UNKNOWN

Tags: Python, Bioimage Analysis, Big Data

Content type: Notebook

guiwitz/DaskCourse

Deep Learning for image analysis - Exercises#

[‘Martin Weigert’]

Licensed UNKNOWN

Tags: Fiji, Artificial Intelligence, Bioimage Analysis

Content type: Notebook

maweigert/zidas_2020_DL_intro_Part_2

DeepProfiler Handbook#

[‘Michael Bornholdt’, ‘Juan Caicedo’, ‘Yu Han’, ‘Nikita Moshkov’, ‘Rebecca Senft’]

Licensed UNKNOWN

Tags: Artificial Intelligence, Bioimage Analysis

Content type: Book

cytomining/DeepProfiler-handbook

https://cytomining.github.io/DeepProfiler-handbook/docs/00-welcome.html

Diffusion Models for Image Restoration - An Introduction#

[‘Anirban Ray’]

Licensed UNKNOWN

Presentation given at the EMBO-DL4MIA 2024, Advanced Topic Seminar, May-11-2024

Tags: Bioimage Analysis, Diffusion Models, Tu Dresden

Content type: Presentation

https://drive.google.com/file/d/1pPVUUMi5w2Ojw_SaBzSQVaXUuIKtQ7Ma/view

EMBL Deep Learning course 2019 exercises and materials#

[‘Valentyna Zinchenko’, ‘Pejman Rasti’, ‘Martin Weigert’, ‘Szymon Stoma’]

Licensed UNKNOWN

Tags: Python, Artificial Intelligence

Content type: Notebook

kreshuklab/teaching-dl-course-2019

EMBL Deep Learning course 2021/22 exercises and materials#

[‘Martin Weigert’, ‘Constantin Pape’]

Licensed UNKNOWN

Tags: Python, Artificial Intelligence

Content type: Notebook

kreshuklab/teaching-dl-course-2022

EMBL Deep Learning course 2023 exercises and materials#

[‘Martin Weigert’, ‘Uwe Schmidt’, ‘Benjamin Gallusser’, ‘Albert Dominguez Mantes’, ‘Buglakova Alyona’]

Licensed UNKNOWN

Tags: Python, Artificial Intelligence

Content type: Notebook

kreshuklab/teaching-dl-course-2023

EuBIAS course 2013: Intensity Dynamics at the Periphery of Nucleus#

[‘Kota Miura’]

Published 2013

Licensed UNKNOWN

Tags: Neubias, Bioimage Analysis

Content type: Tutorial, Book

miura/BIAS_Nucleus_Segmentation

Fundamentals in digital image processing#

[‘Guillaume Witz’]

Licensed UNKNOWN

Tags: Bioimage Analysis

Content type: Notebook

guiwitz/Fundamentals_image_processing

I3D:bio list of online training material#

Licensed UNKNOWN

List of links to training materials by the I3D:bio community.

Tags: Research Data Management

Content type: Collection

https://gerbi-gmb.de/i3dbio/i3dbio-teaching/train-mat/bioimagelist/

Image Data Services at Euro-BioImaging: Community efforts towards FAIR Image Data and Analysis Services#

[‘Aastha Mathur’]

Licensed UNKNOWN

Content type: Slide

https://docs.google.com/presentation/d/1henPIDTpHT3bc1Y26AltItAHJ2C5xCOl/edit#slide=id.p1

Image analysis in Galaxy#

[‘Beatriz Serrano-Solano’, ‘Björn Grüning’]

Licensed UNKNOWN

Tags: Bioimage Analysis

Content type: Slide

https://docs.google.com/presentation/d/1WG_4307XmKsGfWT3taxMvX2rZiG1k0SM1E7SAENJQkI/edit#slide=id.p

ImageJ Macro Introduction#

[‘Anna Klemm’]

Licensed UNKNOWN

Tags: Neubias, Imagej Macro, Bioimage Analysis

Content type: Slide, Code

ahklemm/ImageJMacro_Introduction

Introduction to ImageJ macro programming, Scientific Computing Facility, MPI CBG Dresden#

[‘Robert Haase’, ‘Benoit Lombardot’]

Licensed UNKNOWN

Tags: Imagej, Bioimage Analysis

Content type: Slide

https://git.mpi-cbg.de/scicomp/bioimage_team/coursematerialimageanalysis/tree/master/ImageJMacro_24h_2017-01

Jupyter for interactive cloud computing#

[‘Guillaume Witz’]

Licensed UNKNOWN

Tags: Neubias, Bioimage Analysis

Content type: Slide

https://docs.google.com/presentation/d/1q8q1xE-c35tvCsRXZay98s2UYWwXpp0cfCljBmMFpco/edit#slide=id.ga456d5535c_2_53

Kreshuk Lab’s EMBL EIPP predoc course teaching material#

[‘Adrian Wolny’, ‘Johannes Hugger’, ‘Qin Yu’, ‘Buglakova Alyona’]

Licensed UNKNOWN

Tags: Artificial Intelligence

Content type: Tutorial

kreshuklab/predoc-course

Machine Learning - Deep Learning. Applications to Bioimage Analysis#

[‘Estibaliz Gómez-de-Mariscal’]

Licensed UNKNOWN

Tags: Artificial Intelligence, Bioimage Analysis

Content type: Slide

https://raw.githubusercontent.com/esgomezm/esgomezm.github.io/master/assets/pdf/SPAOM2018/MachineLearning_SPAOMworkshop_public.pdf

Machine Learning Workflow for Imaging Flow Cytometry (IFC)#

Licensed UNKNOWN

Tags: Cellprofiler, Bioimage Analysis

Content type: Tutorial

holgerhennig/machine-learning-IFC

Machine and Deep Learning on the cloud: Segmentation#

[‘Ignacio Arganda-Carreras’]

Licensed UNKNOWN

Tags: Neubias, Artificial Intelligence, Bioimage Analysis

Content type: Slide

https://docs.google.com/presentation/d/1oJoy9gHmUuSmUwCkPs_InJf_WZAzmLlUNvK1FUEB4PA/edit#slide=id.ge3a24e733b_0_54

Materials for EMBL Coding Club Mini-Tutorials#

[‘Jonas Hartmann’, ‘et al.’]

Licensed UNKNOWN

Tags: Python

Content type: Code, Notebook

WhoIsJack/EMBL-CodingClub

https://bio-it.embl.de/Coding%20Club/Curated%20Tutorials/

Metabolic networks modelling with COBRApy#

[‘Karin Sasaki’, ‘Aleksej Zelezniak’]

Licensed UNKNOWN

Tags: Python

Content type: Notebook

karinsasaki/metabolic-networks-modelling

Models and Applications for BioImage.IO#

[‘Wei Ouyang’, ‘et al.’]

Licensed UNKNOWN

imjoy-team/bioimage-io-resources

NEUBIAS Analyst School 2018#

[‘Assaf Zaritsky’, ‘Csaba Molnar’, ‘Vasja Urbancic’, ‘Richard Butler’, ‘Anna Kreshuk’, ‘Vannary Meas-Yedid’]

Licensed UNKNOWN

Tags: Neubias, Bioimage Analysis

Content type: Slide, Code, Notebook

miura/NEUBIAS_AnalystSchool2018

NEUBIAS Bioimage Analyst Course 2017#

[‘Curtis Rueden’, ‘Florian Levet’, ‘J.B. Sibarta’, ‘Alexandre Dafour’, ‘Daniel Sage’, ‘Sebastien Tosi’, ‘Michal Kozubek’, ‘Jean-Yves Tinevez’, ‘Kota Miura’, ‘et al.’]

Licensed UNKNOWN

Tags: Neubias, Bioimage Analysis

Content type: Slide, Tutorial

miura/NEUBIAS_Bioimage_Analyst_Course2017

NEUBIAS Bioimage Analyst School 2019#

[‘Kota Miura’, ‘Chong Zhang’, ‘Jean-Yves Tinevez’, ‘Robert Haase’, ‘Julius Hossein’, ‘Pejamn Rasti’, ‘David Rousseau’, ‘Ignacio Arganda-Carreras’, ‘Siân Culley’, ‘et al.’]

Licensed UNKNOWN

Tags: Neubias, Bioimage Analysis

Content type: Slide, Code, Notebook

miura/NEUBIAS_AnalystSchool2019

NEUBIAS Bioimage Analyst School 2020#

[‘Marion Louveaux’, ‘Stéphane Verger’, ‘Arianne Bercowsky Rama’, ‘Ignacio Arganda-Carreras’, ‘Estibaliz Gómez-de-Mariscal’, ‘Kota Miura’, ‘et al.’]

Licensed UNKNOWN

Tags: Neubias, Bioimage Analysis

Content type: Slide, Code, Notebook

miura/NEUBIAS_AnalystSchool2020

Neubias Academy 2020: Introduction to Nuclei Segmentation with StarDist#

[‘Martin Weigert’, ‘Olivier Burri’, ‘Siân Culley’, ‘Uwe Schmidt’]

Licensed UNKNOWN

Tags: Python, Neubias, Artificial Intelligence, Bioimage Analysis

Content type: Slide, Notebook

maweigert/neubias_academy_stardist

Nextflow Demo Pipelines for Image Processing#

Licensed UNKNOWN

Content type: Code

JaneliaSciComp/nf-demos

OME-Zarr course#

[‘Bugra Oezdemir’, ‘Christian Tischer’]

Licensed UNKNOWN

Content type: Tutorial

https://git.embl.de/oezdemir/course_scripts#ome-zarr-course

OMERO documentation#

Licensed UNKNOWN

Tags: Omero

Content type: Documentation

https://omero.readthedocs.io/en/stable/

Python Workshop - Image Processing#

[‘Karin Sasaki’, ‘Jonas Hartmann’]

Licensed UNKNOWN

Tags: Python

Content type: Code, Notebook

karinsasaki/python-workshop-image-processing

RDM4mic#

Licensed UNKNOWN

Tags: Research Data Management, Omero

Content type: Collection, Video

https://www.youtube.com/@RDM4mic

Scripts_FilopodyanR - a case study for the NEUBIAS TS7 in Szeged#

[‘Marion Louveaux’]

Licensed UNKNOWN

Tags: Neubias, Bioimage Analysis

Content type: Code

marionlouveaux/NEUBIAS2018_TS7

Setting up a data management infrastructure for bioimaging#

[‘Susanne Kunis’, ‘Karen Bernhardt’, ‘Michael Hensel’]

Licensed UNKNOWN

Tags: Nfdi4Bioimage, Research Data Management

Content type: Publication

https://doi.org/10.1515/hsz-2022-0304

Setting up a remote desktop to use Napari in a browser#

[‘Volker Hilsenstein’]

Licensed UNKNOWN

Content type: Tutorial

VolkerH/Jupyter-Napari-Desktop

Source Control Using Git and GitHub#

Licensed UNKNOWN

Content type: Tutorial

JaneliaSciComp/2020AprilGitCourse

TESS training materials#

Licensed UNKNOWN

Tags: Bioinformatics

Content type: Collection

https://tess.elixir-europe.org/materials

Training Deep Learning Models for Vision - Compact Course#

[‘Constantin Pape’, ‘Adrian Wolny’]

Licensed UNKNOWN

Tags: Artificial Intelligence, Bioimage Analysis

constantinpape/training-deep-learning-models-for-vison

What is Bioimage Analysis? An Introduction#

[‘Kota Miura’]

Licensed UNKNOWN

Tags: Neubias, Bioimage Analysis

Content type: Slide

https://www.dropbox.com/s/5abw3cvxrhpobg4/20220923_DefragmentationTS.pdf?dl=0

ZIDAS 2020 Introduction to Deep Learning#

[‘Estibaliz Gómez-de-Mariscal’]

Licensed UNKNOWN

Tags: Artificial Intelligence, Bioimage Analysis

Content type: Slide

esgomezm/zidas2020_intro_DL

i2k-2020-s3-zarr-workshop#

[‘Constantin Pape’, ‘Christian Tischer’]

Licensed UNKNOWN

Content type: Python, Big Data

tischi/i2k-2020-s3-zarr-workshop