Github.com (115)#
2020 BioImage Analysis Survey: Community experiences and needs for the future#
Nasim Jamali, Ellen T. A. Dobson, Kevin W. Eliceiri, Anne E. Carpenter, Beth A. Cimini
Published 2021
Licensed BSD-3-CLAUSE
Tags: Bioimage Analysis
Content type: Publication
2022 MIC Workshop on Bioimage processing with Python#
Guillaume Witz
Licensed UNKNOWN
Tags: Python, Bioimage Analysis
Content type: Notebook
Adding a Workflow to BIAFLOWS#
Sébastien Tosi, Volker Baecker, Benjamin Pavie
Licensed BSD-2-CLAUSE
Tags: Neubias, Bioimage Analysis
Content type: Slide
Analysis of High-Throughput Microscopy Image Data#
Kota Miura, Christoph Schiklenk, Clemens Lakner, Christian Tischer, Aliaksandr Halavatyi
Published 2014
Licensed UNKNOWN
BIDS-lecture-2024#
Robert Haase
Licensed CC-BY-4.0
Training resources for Students at Uni Leipzig who want to dive into bio-image data science with Python. The material developed here between April and July 2024.
Tags: Bioimage Analysis, Deep Learning, Microscopy Image Analysis, Python
Content type: Github Repository
Basics of Image Processing and Analysis#
Kota Miura
Licensed ALL RIGHTS RESERVED
Tags: Bioimage Analysis
Content type: Book
Bio Image Analysis#
Christian Tischer
Licensed UNKNOWN
Tags: Bioimage Analysis
Content type: Slide
Bio-image Analysis ICOB 2023#
Tags: Bioimage Analysis
Content type: Workshop, Collection
Bio-image Analysis Workshop Kioto and Taipei 23/24#
Tags: Bioimage Analysis
Content type: Workshop, Collection
Bio-image Analysis Workshop Taipei#
Tags: Bioimage Analysis
Content type: Workshop, Collection
Bio-image Data Science#
Robert Haase
Licensed CC-BY-4.0
This repository contains training resources for Students at Uni Leipzig who want to dive into bio-image data science with Python.
Tags: Image Data Management, Deep Learning, Microscopy Image Analysis, Python
Content type: Notebook
Bio-image analysis, biostatistics, programming and machine learning for computational biology#
Anna Poetsch, Biotec Dresden, Marcelo Leomil Zoccoler, Johannes Richard Müller, Robert Haase
Licensed CC-BY-4.0
Tags: Python, Bioimage Analysis, Napari
Content type: Notebook
Biomero#
Torec Luik, Johannes Soltwedel
Published 2024-07-24
Licensed APACHE-2.0
The BIOMERO framework, for BioImage analysis in OMERO, allows you to run (FAIR) bioimage analysis workflows directly from OMERO on a high-performance compute (HPC) cluster, remotely through SSH.
Tags: OMERO, Github
Content type: Github Repository
Bridging Imaging Users to Imaging Analysis - A community survey#
Suganya Sivagurunathan, Stefania Marcotti, Carl J Nelson, Martin L Jones, David J Barry, Thomas J A Slater, Kevin W Eliceiri, Beth A Cimini
Published 2023
Licensed BSD-3-CLAUSE
Tags: Bioimage Analysis
Content type: Publication, Preprint
Building a Bioimage Analysis Workflow using Deep Learning#
Estibaliz Gómez-de-Mariscal\
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Slide
CARE/Stardist tutorials for EMBO Practical Course — Computational optical biology 2022#
Martin Weigert
Licensed UNKNOWN
Tags: Python, Artificial Intelligence, Bioimage Analysis
Content type: Notebook
CSBDeep and StarDist @ I2K 2020#
Martin Weigert, Uwe Schmidt
Licensed UNKNOWN
Tags: Python, Artificial Intelligence, Bioimage Analysis
Content type: Notebook
CellProfiler Introduction#
Anna Klemm
Licensed UNKNOWN
Tags: Neubias, Cellprofiler, Bioimage Analysis
Content type: Slide
CellProfiler Practical NeuBIAS Lisbon 2017#
Carolina Wählby, Maxime Bombrun, Christian Tischer
Licensed UNKNOWN
Tags: Neubias, Cellprofiler, Bioimage Analysis
Content type: Tutorial
CellProfiler tutorials#
Licensed BSD-3-CLAUSE
CellProfiler tutorials and guided exercises about translocation, segmentation, pixel-based classification and quality control
Tags: Cellprofiler, Bioimage Analysis
Content type: Notebook
CellTrackColab#
Guillaume Jacquemet
Licensed MIT
Content type: Notebook, Collection
Collection of teaching material for deep learning for (biomedical) image analysis#
Constantin Pape
Licensed MIT
Tags: Artificial Intelligence, Bioimage Analysis
Course on Deep Learning for imaging using PyTorch#
Guillaume Witz
Licensed UNKNOWN
Tags: Python, Bioimage Analysis, Artificial Intelligence
Content type: Notebook
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
DL4MicEverywhere#
Iván Hidalgo, et al.
Licensed CC-BY-4.0
Content type: Notebook, Collection
DL@MBL 2021 Exercises#
Jan Funke, Constantin Pape, Morgan Schwartz, Xiaoyan
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Slide, Notebook
Dask Course#
Guillaume Witz
Licensed UNKNOWN
Tags: Python, Bioimage Analysis, Big Data
Content type: Notebook
Deep Learning Based Segmentation For Biologists#
Licensed AGPL-3.0
Tags: Python, R, Artificial Intelligence
Content type: Notebook
Deep Learning for image analysis - Exercises#
Martin Weigert
Licensed UNKNOWN
Tags: Fiji, Artificial Intelligence, Bioimage Analysis
Content type: Notebook
Deep Vision and Graphics#
Victor Yurchenko, Fedor Ratnikov, Viktoriia Checkalina
Licensed MIT
Tags: Python, Artificial Intelligence
Content type: Notebook
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
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
EMBL Deep Learning course 2021/22 exercises and materials#
Martin Weigert, Constantin Pape
Licensed UNKNOWN
Tags: Python, Artificial Intelligence
Content type: Notebook
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
EmbedSeg Repository#
Manan Lalit, Joran Deschamps, Florian Jug, Ajinkya Kulkarni
Licensed CC-BY-NC-4.0
Code Implementation for EmbedSeg, an Instance Segmentation Method for Microscopy Images
Tags: Bioimage Analysis, Instance Segmentation
Content type: Github Repository
EuBIAS course 2013: Intensity Dynamics at the Periphery of Nucleus#
Kota Miura
Published 2013
Licensed UNKNOWN
Tags: Neubias, Bioimage Analysis
Content type: Tutorial, Book
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/
FriendsDontLetFriends#
C. Li
Published 2024-03-10T15:34:07+00:00
Licensed MIT
Friends don’t let friends make certain types of data visualization - What are they and why are they bad.
Tags: Visualization
Content type: Github Repository
Fundamentals in digital image processing#
Guillaume Witz
Licensed UNKNOWN
Tags: Bioimage Analysis
Content type: Notebook
Fundamentals of image analysis in Python with scikit-image, napari, and friends#
Juan Nunez-Iglesias
Licensed BSD-3-CLAUSE
Tags: Python, Bioimage Analysis
Content type: Notebook
Galaxy Training Material#
Licensed MIT
Content type: Slides, Tutorial
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 workshop material - Lazy Parallel Processing and Visualization of Large Data with ImgLib2, BigDataViewer, the N5-API, and Spark#
Stephan Saalfeld, Tobias Pietzsch
Published None
Licensed APACHE-2.0
Tags: Training
Content type: Workshop, Notebook, Github Repository
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
IAFIG-RMS Python for Bioimage Analysis Course#
Aurelien Barbotin, Chas Nelson, Dominic Waithe, Ola (Alexandra) Tarkowska, Mikolaj Kundegorski, Stephen Cross, Todd Fallesen
Licensed GPL-3.0
Tags: Bioimage Analysis
Content type: Notebook
ITKElastix Examples#
Licensed APACHE-2.0
Tags: Bioimage Analysis
Image Processing with Python#
Jacob Deppen, Kimberly Meechan, David Palmquist, Ulf Schiller, Robert Turner, Marianne Corvellec, Toby Hodges, et al.
Licensed CC-BY-4.0
Tags: Python, Bioimage Analysis
Content type: Collection
Image analysis and visualization in Python with scikit-image, napari, and friends#
Juan Nunez-Iglesias
Licensed BSD-3-CLAUSE
Tags: Python, Bioimage Analysis
Content type: Notebook
Image analysis course material#
Christian Tischer
Licensed MIT
Training materials about image registration, big warp and elastix
Image processing for beginners#
Guillaume Witz
Licensed BSD-3-CLAUSE
Tags: Python, Bioimage Analysis
Content type: Notebook
Image processing with Python#
Guillaume Witz
Licensed MIT
Series of Notebooks exposing how to do mostly basic and some advanced image processing using Python. It uses standard packages (Numpy, Maplotlib) and for the image processing parts is heavily based on the scikit-image package.
Tags: Python
Content type: Notebook
Image-based Profiling Handbook#
Beth Cimini, Tim Becker, Shantanu Singh, Gregory Way, Hamdah Abbasi, Callum Tromans-Coia
Licensed CC0-1.0
Tags: Bioimage Analysis
Content type: Book
ImageJ Macro Introduction#
Anna Klemm
Licensed UNKNOWN
Tags: Neubias, Imagej Macro, Bioimage Analysis
Content type: Slide, Code
Introduction to Deep Learning for Microscopy#
Costantin Pape
Licensed MIT
This course consists of lectures and exercises that teach the background of deep learning for image analysis and show applications to classification and segmentation analysis problems.
Tags: Deep Learning, Pytorch, Segmentation, Python
Content type: Notebook
Introduction to Image Analysis with Fiji#
Robert Haase, Benoit Lombardot
Licensed CC-BY-NC-4.0
Tags: Imagej, Fiji, Bioimage Analysis
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
Lecture-materials of the DeepLife course#
Carl Herrmann, annavonbachmann, David Hoksza, Martin Schätz, Dario Malchiodi, jnguyenvan, Britta Velten, Elodie Laine, JanaBraunger, barwil
Published 2023-12-06
Licensed UNKNOWN
Tags: Bioinformatics
Content type: Github Repository, Slides, Notebook
Machine Learning Workflow for Imaging Flow Cytometry (IFC)#
Licensed UNKNOWN
Tags: Cellprofiler, Bioimage Analysis
Content type: Tutorial
Materials for EMBL Coding Club Mini-Tutorials#
Jonas Hartmann, et al.
Licensed UNKNOWN
Tags: Python
Content type: Code, Notebook
Metabolic networks modelling with COBRApy#
Karin Sasaki, Aleksej Zelezniak
Licensed UNKNOWN
Tags: Python
Content type: Notebook
Models and Applications for BioImage.IO#
Wei Ouyang, et al.
Licensed UNKNOWN
Multiplexed tissue imaging - tools and approaches#
Agustín Andrés Corbat, OmFrederic, Jonas Windhager, Kristína Lidayová
Licensed CC-BY-4.0
Material for the I2K 2024 “Multiplexed tissue imaging - tools and approaches” workshop
Tags: Bioimage Analysis, Microscopy Image Analysis
Content type: Github Repository, Slides, Workshop
BIIFSweden/I2K2024-MTIWorkshop
https://docs.google.com/presentation/d/1R9-4lXAmTYuyFZpTMDR85SjnLsPZhVZ8/edit#slide=id.p1
NEUBIAS Academy @HOME: Interactive Bioimage Analysis with Python and Jupyter#
Licensed BSD-3-CLAUSE
Tags: Python, Neubias, Bioimage Analysis
Content type: Notebook
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
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
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
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
NFDI4Bioimage - TA3-Hackathon - UoC-2023 (Cologne Hackathon)#
Mohamed M. Abdrabbou, Mehrnaz Babaki, Tom Boissonnet, Michele Bortolomeazzi, Eik Dahms, Vanessa A. F. Fuchs, Moritz Hoevels, Niraj Kandpal, Christoph Möhl, Joshua A. Moore, Astrid Schauss, Andrea Schrader, Torsten Stöter, Julia Thönnißen, Monica Valencia-S., H. Lukas Weil, Jens Wendt and Peter Zentis
Licensed CC-BY-4.0
Tags: Arc, Dataplant, Hackathon, Nfdi4Bioimage, OMERO, Python, Research Data Management
Content type: Event, Publication, Documentation
NLP Course#
Yandex School of Data Analysis
Licensed MIT
YSDA course in Natural Language Processing
Tags: Natural Language Processing
Content type: Github Repository
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
NeubiasPasteur2023_AdvancedCellPose#
Gaelle Letort
Licensed BSD-3-CLAUSE
Tutorial for running CellPose advanced functions
Tags: Cellpose, Segmentation
Content type: Github Repository
Nextflow Demo Pipelines for Image Processing#
Licensed UNKNOWN
Content type: Code
OMERO - HCS analysis pipeline using Jupyter Notebooks#
Riccardo Massei
Licensed MIT
Material and solutions for the course ‘Bioimage data management and analysis with OMERO’ held in Heidelberg (13th May 2024) - Module 3 (1.45 pm - 3.45 pm): OMERO and Jupyter Notebooks. Main goal of the workflow is to show the potential of JN to perform reproducible image analysis in connection with an OMERO instance. In this specific example, we are performing a simple nuclei segmentation from raw images uploaded in OMERO.
Tags: Teaching, Bioimage Analysis, Notebooks, Python, OMERO
Content type: Github Repository
ONBI Image Analysis Course#
Mark Jenkinson, Jens Rittscher, Dominic Waithe
Licensed GPL-2.0
This repository contains the materials for the University of Oxford DTC ONBI Image Analysis course.
Tags: Python, Bioimage Analysis
Content type: Notebook
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
Omero Deployment examples#
Licensed BSD-2-CLAUSE
Tags: OMERO
Content type: Collection
Online_R_learning#
C. Li
Published 2023-07-09T06:27:14+00:00
Licensed CC0-1.0
Online R learning for applied statistics
Tags: Statistics
Content type: Github Repository
Plugin “omero-batch-plugin”#
Licensed GPL-2.0
An ImageJ plugin to run a script or macro on a batch of images from/to OMERO.
Tags: OMERO, Imagej, Imagej Macro, Github
Content type: Github Repository
Plugin “omero-cli-transfer”#
Erick Martins Ratamero, Jean-Marie Burel, Will Moore, Guillaume Gay, Christoph Moehl, et al.
Published 2024-09-14
Licensed GPL-2.0
An OMERO CLI plugin for creating and using transfer packets between OMERO servers.
Tags: OMERO
Content type: Github Repository
Plugin “simple-omero-client”#
Pierre Pouchin, Rdornier, kekunn, Jean-Marie Burel
Licensed GPL-2.0
A wrapper library which can be called from scripts in Fiji, but can mostly be used in Maven projects to wrap calls to the underlying OMERO Java Gateway.
Tags: OMERO, Github, Fiji
Content type: Github Repository
PoL Bio-Image Analysis Training School on GPU-Accelerated Image Analysis#
Stephane Rigaud, Brian Northan, Till Korten, Neringa Jurenaite, Apurv Deepak Kulkarni, Peter Steinbach, Sebastian Starke, Johannes Soltwedel, Marvin Albert, Robert Haase
Licensed CC-BY-4.0
This repository hosts notebooks, information and data for the GPU-Accelerated Image Analysis Track of the PoL Bio-Image Analysis Symposium.
Tags: Gpu, Clesperanto, Dask, Python
Content type: Notebook
BiAPoL/PoL-BioImage-Analysis-TS-GPU-Accelerated-Image-Analysis
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
Python BioImage Analysis Tutorial#
Jonas Hartmann
Licensed MIT
Tags: Python, Bioimage Analysis
Python Workshop - Image Processing#
Karin Sasaki, Jonas Hartmann
Licensed UNKNOWN
Tags: Python
Content type: Code, Notebook
Python for Microscopists#
Sreenivas Bhattiprolu
Licensed MIT
Tags: Python, Bioimage Analysis
Content type: Notebook, Collection
QuPath for Python programmers#
Alan O’Callaghan, Léo Leplat
Published 2024-10-23
Licensed UNKNOWN
These are the notebooks and associated files for the i2k 2024 QuPath for Python programmers workshop.
Tags: Python, Notebooks, Open Source Software, Bioimage Analysis
Content type: Github Repository, Notebook, Collection
RDM4Mic Presentations#
Licensed CC-BY-4.0
Tags: Research Data Management
Content type: Collection
RDM_system_connector#
SaibotMagd
Licensed UNKNOWN
This tool is intended to link different research data management platforms with each other.
Tags: Research Data Management, Image Data Management
Content type: Github Repository
Scientific Visualization: Python + Matplotlib#
Nicolas P. Rougier
Licensed CC-BY-ND-SA-4.0
Tags: Python
Content type: Book
Scipy Cookbook#
Pauli Virtanen et al.
Licensed BSD-3-CLAUSE
This is a conversion and second life of SciPy Cookbook as a bunch of Ipython notebooks.
Tags: Bioimage Analysis
Content type: Github Repository
Scripts_FilopodyanR - a case study for the NEUBIAS TS7 in Szeged#
Marion Louveaux
Licensed UNKNOWN
Tags: Neubias, Bioimage Analysis
Content type: Code
Setting up a remote desktop to use Napari in a browser#
Volker Hilsenstein
Licensed UNKNOWN
Content type: Tutorial
SimpleITK-Notebooks#
Ziv Yaniv et al.
Licensed APACHE-2.0 LICENSE
Jupyter notebooks for learning how to use SimpleITK
Tags: Bioimage Analysis, Simpleitk
Content type: Github Repository
Source Control Using Git and GitHub#
Licensed UNKNOWN
Content type: Tutorial
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
Training Deep Learning Models for Vision - Compact Course#
Constantin Pape, Adrian Wolny
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
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
Workshop-June2024-Madrid#
Licensed MIT
Tags: Bioimage Analysis
Content type: Workshop, Collection
YMIA - Python-Based Event Series Training Material#
Riccardo Massei, Robert Haase, ENicolay
Published None
Licensed MIT
This repository offer access to teaching material and useful resources for the YMIA - Python-Based Event Series.
Tags: Python, Large Language Models, Prompt Engineering, Biabob, Bioimage Analysis, Microscopy Image Analysis
Content type: Github Repository, Slides
ZEN & Python workshop#
Licensed GPL-3.0
Tags: Python, Napari, Bioimage Analysis
Content type: Collection, Notebook
ZIDAS 2020 Introduction to Deep Learning#
Estibaliz Gómez-de-Mariscal
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Slide
ZeroCostDL4Mic: exploiting Google Colab to develop a free and open-source toolbox for Deep-Learning in microscopy#
Lucas von Chamier, Romain F. Laine, Johanna Jukkala, Christoph Spahn, Daniel Krentzel, Elias Nehme, Martina Lerche, Sara Hernández-pérez, Pieta Mattila, Eleni Karinou, Séamus Holden, Ahmet Can Solak, Alexander Krull, Tim-Oliver Buchholz, Martin L Jones, Loic Alain Royer, Christophe Leterrier, Yoav Shechtman, Florian Jug, Mike Heilemann, Guillaume Jacquemet, Ricardo Henriques
Licensed MIT
Content type: Notebook, Collection
bioformats2raw Converter#
Melissa Linkert, Chris Allan, Josh Moore, Sébastien Besson, David Gault, et al.
Licensed GPL-2.0
Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-NGFF specification.
Tags: Open Source Software, Bioimage Data
Content type: Application, Github Repository
i2k-2020-s3-zarr-workshop#
Constantin Pape, Christian Tischer
Licensed UNKNOWN
Tags: Python, Big Data
Content type: Github Repository
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
numpy pandas course#
Guillaume Witz
Licensed BSD-3-CLAUSE
Tags: Python
Content type: Notebook
ome-ngff-validator#
Will Moore, Josh Moore, Yaroslav Halchenko, Sébastien Besson
Published 2022-09-29
Licensed BSD-2-CLAUSE
Web page for validating OME-NGFF files.
Tags: Bioimage Data
Content type: Github Repository, Application
quantixed/TheDigitalCell: First complete code set#
Stephen Royle
Published 2019-04-17
Licensed GPL-3.0
First complete code set for The Digital Cell book.
Tags: Bioimage Analysis
Content type: Code
raw2ometiff Converter#
Melissa Linkert, Chris Allan, Sébastien Besson, Josh Moore
Licensed GPL-2.0
Java application to convert a directory of tiles to an OME-TIFF pyramid. This is the second half of iSyntax/.mrxs => OME-TIFF conversion.
Tags: Open Source Software, Bioimage Data
Content type: Application, Github Repository
scikit-learn MOOC#
Loïc Estève et al.
Licensed CC-BY-4.0
Machine learning in Python with scikit-learn MOOC
Tags: Bioimage Analysis, Machine Learning
Content type: Github Repository
skimage-tutorials#
Juan Nunez-Iglesias et al.
Licensed CC0 1.0 UNIVERSAL
skimage-tutorials - a collection of tutorials for the scikit-image package.
Tags: Bioimage Analysis, Scikit-Image
Content type: Github Repository
training-resources#
Christian Tischer, Antonio Politi, Toby Hodges, maulakhan, grinic, bugraoezdemir, Tim-Oliver Buchholz, Elnaz Fazeli, Aliaksandr Halavatyi, Dominik Kutra, Stefania Marcotti, AnniekStok, Felix, jhennies, Severina Klaus, Martin Schorb, Nima Vakili, Sebastian Gonzalez Tirado, Stefan Helfrich, Yi Sun, Ziqiang Huang, Jan Eglinger, Constantin Pape, Joel Lüthi, Matt McCormick, Oane Gros
Published 2020-04-23T07:51:38+00:00
Licensed CC-BY-4.0
Resources for teaching/preparing to teach bioimage analysis
Tags: Bioimageanalysis, Neurobias
Content type: Github Repository