Tutorial (40)#
CellProfiler Practical NeuBIAS Lisbon 2017#
Carolina Wählby, Maxime Bombrun, Christian Tischer
Licensed UNKNOWN
Tags: Neubias, Cellprofiler, Bioimage Analysis
Content type: Tutorial
Creating Workflows and Advanced Workflow Options#
Licensed CC-BY-4.0
Tags: Workflow
Content type: Tutorial, Online Tutorial
Data Carpentry for Biologists#
Licensed [‘CC-BY-4.0’, ‘MIT’]
Content type: Tutorial, Code
Docker Mastery - with Kubernetes + Swarm from a Docker Captain#
Bret Fisher
Licensed UNKNOWN
In this course you will learn how to use Docker, Compose and Kubernetes on your machine for better software building and testing.
Tags: Docker, Training
Content type: Videos, Tutorial, Online Course
Dokumentation und Anleitung zum elektronischen Laborbuch (eLabFTW)#
Lienhard Wegewitz, F. Strauß
Published 2020-03-23
Licensed AGPL-3.0
Documentation for eLabFTW. With eLabFTW you get a secure, modern and compliant system to track your experiments efficiently but also manage your lab with a powerful and versatile database.
Tags: Research Data Management
Content type: Documentation, Document, Tutorial
https://www.fdm.tu-clausthal.de/fileadmin/FDM/documents/Manual_eLab_v0.3_20200323.pdf
EuBIAS course 2013: Intensity Dynamics at the Periphery of Nucleus#
Kota Miura
Published 2013
Licensed UNKNOWN
Tags: Neubias, Bioimage Analysis
Content type: Tutorial, Book
Euro-BioImaging’s Guide to FAIR BioImage Data - Practical Tasks#
Isabel Kemmer, Euro-BioImaging ERIC
Published 2024-06-04
Licensed CC-BY-4.0
Hands-on exercises on FAIR Bioimage Data from the interactive online workshop “Euro-BioImaging’s Guide to FAIR BioImage Data 2024” (https://www.eurobioimaging.eu/news/a-guide-to-fair-bioimage-data-2024/). Types of tasks included: FAIR characteristics of a real world dataset Data Management Plan (DMP) Journal Policies on FAIR data sharing Ontology search Metadata according to REMBI scheme (Image from: Sarkans, U., Chiu, W., Collinson, L. et al. REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology. Nat Methods 18, 1418–1422 (2021). https://doi.org/10.1038/s41592-021-01166-8) Matching datasets to bioimage repositories Browsing bioimage repositories
Tags: Bioimage Analysis, FAIR-Principles, Research Data Management
Content type: Slides, Tutorial
Euro-BioImaging’s Template for Research Data Management Plans#
Isabel Kemmer, Euro-BioImaging ERIC
Published 2024-06-04
Licensed CC-BY-4.0
Euro-BioImaging has developed a Data Management Plan (DMP) template with questions tailored to bioimaging research projects. Outlining data management practices in this way ensures traceability of project data, allowing for a continuous and unambiguous flow of information throughout the research project. This template can be used to satisfy the requirement to submit a DMP to certain funders. Regardless of the funder, Euro-BioImaging users are encouraged to provide a DMP and can use this template accordingly. This DMP template is available as a fillable PDF with further instructions and sample responses available by hovering over the fillable fields.
Tags: Bioimage Analysis, FAIR-Principles, Research Data Management
Content type: Collection, Tutorial
Example Pipeline Tutorial#
Tim Monko
Published 2024-10-28
Licensed BSD-3-CLAUSE
Napari-ndev is a collection of widgets intended to serve any person seeking to process microscopy images from start to finish. The goal of this example pipeline is to get the user familiar with working with napari-ndev for batch processing and reproducibility (view Image Utilities and Workflow Widget).
Tags: Napari, Microscopy Image Analysis, Bioimage Analysis
Content type: Documentation, Github Repository, Tutorial
https://timmonko.github.io/napari-ndev/tutorial/01_example_pipeline/
Finding and Choosing a Data Repository#
Christian Schmidt
Published 2023-07-01
Licensed UNKNOWN
Funding agencies may demand that original source data of a publication be published, too. So the question is - where should one publish the data? And how does it get there?
Tags: I3Dbio, Research Data Management
Content type: Tutorial
https://gerbi-gmb.de/2023/06/01/finding-and-choosing-a-repository/
Finding and using publicly available data#
Anna Swan
Published 2024-01-01
Licensed CC-BY-4.0
Sharing knowledge and data in the life sciences allows us to learn from each other and built on what others have discovered. This collection of online courses brings together a variety of training, covering topics such as biocuration, open data, restricted access data and finding publicly available data, to help you discover and make the most of publicly available data in the life sciences.
Tags: Open Science, Teaching, Sharing
Content type: Collection, Tutorial, Videos
https://www.ebi.ac.uk/training/online/courses/finding-using-public-data/
Galaxy Training#
Published None
Licensed CC-BY-4.0
Collection of tutorials developed and maintained by the worldwide Galaxy community.
Tags: Bioimage Analysis, Data Analysis
Content type: Collection, Tutorial
Galaxy Training Material#
Licensed MIT
Content type: Slides, Tutorial
Galaxy workflows#
Licensed CC0-1.0
A workflow is a chain of analysis steps. In Galaxy, we can create a workflow from an existing analysis history, or we can create one visually by adding tools to a canvas. This tutorial covers building a workflow to analyse a bacterial genome, from input FASTQ sequencing reads to assembly, annotation, and visualization.
Tags: Workflow
Content type: Online Tutorial, Tutorial
https://galaxy-au-training.github.io/tutorials/modules/workflows/
Glencoe Software Webinars#
Chris Allan, Emil Rozbicki
Licensed UNKNOWN
Example Workflows / usage of the Glencoe Software.
Tags: OMERO, Training
Content type: Videos, Tutorial, Collection
I2K 2024: clEsperanto - GPU-Accelerated Image Processing Library#
Stephane Rigaud, Robert Haase
Licensed BSD-3-CLAUSE
Course and material for the clEsperanto workshop presented at I2K 2024 @ Human Technopol (Milan, Italy). The workshop is an hands-on demo of the clesperanto project, focussing on how to use the library for users who want use GPU-acceleration for their Image Processing pipeline.
Tags: Clesperanto, Training, Bioimage Analysis, Notebooks, Workflow
Content type: Github Repository, Workshop, Tutorial, Notebook
I2K2024(virtual) - Bio-Image Analysis Code Generation#
Robert Haase
Licensed BSD-3-CLAUSE
This repository contains training materials for the Tutorial “Bio-Image Analysis Code Generation” at the From Images To Knowledge (I2K) Conference (virtual) October 28th-30th 2024.
Tags: Bioimage Analysis, Notebooks, Biabob
Content type: Github Repository, Tutorial, Notebook
Image Processing with Python#
Mark Meysenburg, Toby Hodges, Dominik Kutra, Erin Becker, David Palmquist, et al.
Licensed CC-BY-4.0
This lesson shows how to use Python and scikit-image to do basic image processing.
Tags: Segmentation, Bioimage Analysis, Training, Python, Scikit-Image, Image Segmentation
Content type: Tutorial, Workflow
KNIME Image Processing#
None
Licensed GPLV3
The KNIME Image Processing Extension allows you to read in more than 140 different kinds of images and to apply well known methods on images, like preprocessing. segmentation, feature extraction, tracking and classification in KNIME.
Tags: Imagej, OMERO, Bioimage Data, Workflow
Content type: Tutorial, Online Tutorial, Documentation
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
Machine Learning Workflow for Imaging Flow Cytometry (IFC)#
Licensed UNKNOWN
Tags: Cellprofiler, Bioimage Analysis
Content type: Tutorial
Making your project citable#
A tutorial explaining how to make Github repositories citable by automatically creating DOIs using the Github-Zenodo integration.
Tags: Sharing, Citing, Research Data Management
Content type: Tutorial
https://coderefinery.github.io/github-without-command-line/doi/
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
OME-Zarr course#
Bugra Oezdemir, Christian Tischer
Licensed UNKNOWN
Content type: Tutorial
Object Tracking and Track Analysis using TrackMate and CellTracksColab#
Joanna Pylvänäinen
Published None
Licensed GPL-3.0
I2K 2024 workshop materials for “Object Tracking and Track Analysis using TrackMate and CellTracksColab”
Tags: Bioimage Analysis, Training
Content type: Github Repository, Tutorial, Workshop, Slides
Prompt-Engineering-LLMs-Course#
Published 2024-09-11T07:45:30+00:00
Licensed MIT
Tags: Llms, Prompt Engineering, Code Generation
Content type: Github Repository, Tutorial
HelmholtzAI-Consultants-Munich/Prompt-Engineering-LLMs-Course
Research data - what are the key issues to consider when publishing this kind of material?#
Licensed UNKNOWN
The website offers detailed advice on publishing research data, focusing on key issues like data management, FAIR data principles, legal considerations, and repository selection.
Tags: Research Data Management, FAIR-Principles, Licensing
Content type: Tutorial
https://www.publisso.de/en/advice/publishing-advice-faqs/research-data
SWC/GCNU Software Skills#
Licensed CC-BY-4.0
Computational skills training at the UCL Sainsbury Wellcome Centre and Gatsby Computational Neuroscience Unit, delivered by members of the Neuroinformatics Unit.
Tags: Training
Content type: Collection, Online Course, Videos, Tutorial
Setting up a remote desktop to use Napari in a browser#
Volker Hilsenstein
Licensed UNKNOWN
Content type: Tutorial
Software Citation with CITATION.cff#
How to make your Github repository citable by adding a citation.cff file.
Tags: Sharing, Citing, Research Data Management
Content type: Tutorial
https://the-turing-way.netlify.app/communication/citable/citable-cff.html
Source Control Using Git and GitHub#
Licensed UNKNOWN
Content type: Tutorial
Submitting data to the BioImage Archive#
Licensed CC0-1.0
To submit, you’ll need to register an account, organise and upload your data, prepare a file list, and then submit using our web submission form. These steps are explained here.
Tags: Research Data Management, Image Data Management, Bioimage Data
Content type: Tutorial, Video
Teaching Bioimage Analysis with Python#
Rafael Camacho
Licensed MIT
Tags: Python, Bioimage Analysis
Content type: Tutorial
Teaching ImageJ FIJI#
Rafael Camacho
Licensed MIT
Tags: Fiji, Bioimage Analysis
Content type: Tutorial
Ultrack I2K 2024 Workshop Materials#
Jordão Bragantini, Teun Huijben
Licensed BSD3-CLAUSE
Tags: Segmentation, Bioimage Analysis, Training
Content type: Workshop, Github Repository, Tutorial
Virtual-I2K-2024-multiview-stitcher#
Published 2024-10-30T07:38:11+00:00
Licensed BSD-3-CLAUSE
Repository accompanying the multiview-stitcher tutorial for Virtual I2K 2024
Tags: Big Data, Bioimageanalysis
Content type: Github Repository, Tutorial
cba-support-template#
Arif Khan, Christian Tischer, Sebastian Gonzalez, Dominik Kutra, Felix Schneider, et al.
Published 2021-12-01
Licensed MIT
Tags: Workflow, Research Data Management
Content type: Tutorial
introduction-to-generative-ai#
Bruna Piereck, Alexander Botzki
Published 2024-09-27T14:38:51+00:00
Licensed CC-BY-4.0
Course repository for Strategic Use of Generative AI
Tags: Artificial Intelligence
Content type: Github Repository, Tutorial
nextflow-workshop#
Tuur Muyldermans, Kris Davie, Alexander, Nicolas Vannieuwkerke, Kobe Lavaerts, Marcel Ribeiro-Dantas, Bruna Piereck, Steff Taelman
Published 2023-03-29T10:40:04+00:00
Licensed CC-BY-4.0
Nextflow workshop materials March 2023
Tags: Workflow, Nextflow
Content type: Github Repository, Tutorial