Github.com (151)#
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, Exclude From Dalia
Content type: Publication
2022 MIC Workshop on Bioimage processing with Python#
Guillaume Witz
Licensed UNKNOWN
Tags: Python, Bioimage Analysis, Include In Dalia
Content type: Notebook
2023_CourseImageAnalysis_NanoCell#
Fernanda Fossa
Published 2023-08-24T10:15:11+00:00
Licensed MIT
Course about image analysis with materials in English and videos in Portuguese.
Tags: Cell Profiler, Bioimage Analysis, Include In Dalia
Content type: Github Repository
Adding a Workflow to BIAFLOWS#
Sébastien Tosi, Volker Baecker, Benjamin Pavie
Licensed BSD-2-CLAUSE
Tags: Neubias, Bioimage Analysis, Exclude From Dalia
Content type: Slides
Advanced scripting with Fiji#
Joran Deschamps, Damian Dalle Nogare
Published 2023-06-14T08:25:35+00:00
Licensed BSD-3-CLAUSE
Tags: Fiji, Include In Dalia
Content type: Github Repository
Analysis of High-Throughput Microscopy Image Data#
Kota Miura, Christoph Schiklenk, Clemens Lakner, Christian Tischer, Aliaksandr Halavatyi
Published 2014
Licensed UNKNOWN
Tags: Bioimage Analysis, Include In Dalia
BCCD Dataset#
Shenggan Gan, Nicolas Chen
Published 2017-12-07
Licensed MIT
BCCD Dataset is a small-scale dataset for blood cells detection.
Tags: Ai-Ready, Exclude From Dalia
Content type: Data
BHG2023-OMERO-ARC#
Andrea Schrader, Michele Bortolomeazzi, Niraj Kandpal, Torsten Stöter, Kevin Schneider, Peter Zentis, Josh Moore, Jeam-Marie Burel, Tom Boissonnet
Licensed CC-BY-4.0
Repository for documentation during the 2nd de.NBI BioHackathon Germany - 11.-15.12.2023 - OMERO-ARC project (in short: BHG2023-OMERO-ARC)
Tags: Nfdi4Bioimage, Bioinformatics, OMERO, Exclude From Dalia
Content type: Github Repository
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, Artificial Intelligence, Python, Exclude From Dalia
Content type: Github Repository
Basics of Image Processing and Analysis#
Kota Miura
Licensed ALL RIGHTS RESERVED
Tags: Bioimage Analysis, Include In Dalia
Content type: Book
Bio Image Analysis#
Christian Tischer
Licensed UNKNOWN
Tags: Exclude From Dalia
Content type: Slides
Bio-image Analysis ICOB 2023#
Tags: Bioimage Analysis, Exclude From Dalia
Content type: Workshop, Collection
Bio-image Analysis Workshop Kioto and Taipei 23/24#
Tags: Bioimage Analysis, Include In Dalia
Content type: Workshop, Collection
Bio-image Analysis Workshop Taipei#
Tags: Bioimage Analysis, Include In Dalia
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: Research Data Management, Artificial Intelligence, Bioimage Analysis, Python, Include In Dalia
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, Include In Dalia
Content type: Notebook
Bioimaging AI Textbook#
Rachel Lee, Owen Puls, Wei Ouyang, Beth Cimini
Published 2025-02-20
Licensed BSD-3-CLAUSE
This is a repository containing a textbook written for BioImaging scientists and other microscopists.
Tags: Bioimage Analysis, Artificial Intelligence, Include In Dalia
Content type: Book, Github Repository
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, Exclude From Dalia
Content type: Github Repository
Breast Cancer Semantic Segmentation (BCSS) dataset#
Mohamed Amgad, Habiba Elfandy, Hagar Hussein, Lamees A Atteya, Mai A T Elsebaie, Lamia S Abo Elnasr, Rokia A Sakr, Hazem S E Salem, Ahmed F Ismail, Anas M Saad, Joumana Ahmed, Maha A T Elsebaie, Mustafijur Rahman, Inas A Ruhban, Nada M Elgazar, Yahya Alagha, Mohamed H Osman, Ahmed M Alhusseiny, Mariam M Khalaf, Abo-Alela F Younes, Ali Abdulkarim, Duaa M Younes, Ahmed M Gadallah, Ahmad M Elkashash, Salma Y Fala, Basma M Zaki, Jonathan Beezley, Deepak R Chittajallu, David Manthey, David A Gutman, Lee A D Cooper
Published 2019-11-09
Licensed CC0-1.0
This repo contains the necessary information and download instructions to download the dataset associated with the paper: Amgad M, Elfandy H, …, Gutman DA, Cooper LAD. Structured crowdsourcing enables convolutional segmentation of histology images. Bioinformatics. 2019. doi: 10.1093/bioinformatics/btz083. This data can be visualized in a public instance of the Digital Slide Archive at this link. If you click the “eye” image icon in the Annotations panel on the right side of the screen, you will see the results of a collaborative annotation.
Tags: Ai-Ready, Exclude From Dalia
Content type: Data
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, Exclude From Dalia
Content type: Publication, Preprint
Building a Bioimage Analysis Workflow using Deep Learning#
Estibaliz Gómez-de-Mariscal
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis, Include In Dalia
Content type: Slides
CARE/Stardist tutorials for EMBO Practical Course — Computational optical biology 2022#
Martin Weigert
Licensed UNKNOWN
Tags: Python, Artificial Intelligence, Bioimage Analysis, Include In Dalia
Content type: Notebook
CSBDeep and StarDist @ I2K 2020#
Martin Weigert, Uwe Schmidt
Licensed UNKNOWN
Tags: Python, Artificial Intelligence, Bioimage Analysis, Include In Dalia
Content type: Notebook
CellProfiler Introduction#
Anna Klemm
Licensed UNKNOWN
Tags: Neubias, Cellprofiler, Bioimage Analysis, Include In Dalia
Content type: Slides
CellProfiler Practical NeuBIAS Lisbon 2017#
Carolina Wählby, Maxime Bombrun, Christian Tischer
Licensed UNKNOWN
Tags: Neubias, Cellprofiler, Bioimage Analysis, Include In Dalia
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, Include In Dalia
Content type: Notebook
CellTrackColab#
Guillaume Jacquemet
Licensed MIT
Tags: Exclude From Dalia
Content type: Notebook, Collection
Collection of teaching material for deep learning for (biomedical) image analysis#
Constantin Pape
Licensed MIT
Tags: Artificial Intelligence, Bioimage Analysis, Include In Dalia
Course on Deep Learning for imaging using PyTorch#
Guillaume Witz
Licensed UNKNOWN
Tags: Python, Bioimage Analysis, Artificial Intelligence, Include In Dalia
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, Exclude From Dalia
Content type: Notebook
DL4MicEverywhere#
Iván Hidalgo, et al.
Licensed CC-BY-4.0
Tags: Bioimage Analysis, Exclude From Dalia
Content type: Notebook, Collection
DL4Proteins-notebooks#
Michael Chungyoun, Courtney Thomas, Britnie Carpentier, GabeAu79, puv-sreev, Jeffrey Gray
Published 2024-09-04T12:24:24+00:00
Colab Notebooks covering deep learning tools for biomolecular structure prediction and design
Tags: Bioinformatics, Exclude From Dalia
Content type: Github Repository, Collection
DL@MBL 2021 Exercises#
Jan Funke, Constantin Pape, Morgan Schwartz, Xiaoyan
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis, Exclude From Dalia
Content type: Slides, Notebook
Dask Course#
Guillaume Witz
Licensed UNKNOWN
Tags: Python, Bioimage Analysis, Big Data, Exclude From Dalia
Content type: Notebook
Deep Learning Based Segmentation For Biologists#
Licensed AGPL-3.0
Tags: Python, R, Artificial Intelligence, Include In Dalia
Content type: Notebook
Deep Learning for image analysis - Exercises#
Martin Weigert
Licensed UNKNOWN
Tags: Fiji, Artificial Intelligence, Bioimage Analysis, Include In Dalia
Content type: Notebook
Deep Vision and Graphics#
Victor Yurchenko, Fedor Ratnikov, Viktoriia Checkalina
Licensed MIT
Tags: Python, Artificial Intelligence, Include In Dalia
Content type: Notebook
DeepProfiler Handbook#
Michael Bornholdt, Juan Caicedo, Yu Han, Nikita Moshkov, Rebecca Senft
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis, Include In Dalia
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, Include In Dalia
Content type: Notebook
EMBL Deep Learning course 2021/22 exercises and materials#
Martin Weigert, Constantin Pape
Licensed UNKNOWN
Tags: Python, Artificial Intelligence, Include In Dalia
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, Include In Dalia
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, Exclude From Dalia
Content type: Github Repository
EuBIAS course 2013: Intensity Dynamics at the Periphery of Nucleus#
Kota Miura
Published 2013
Licensed UNKNOWN
Tags: Neubias, Bioimage Analysis, Include In Dalia
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, Bioimage Analysis, Exclude From Dalia
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, Include In Dalia
Content type: Github Repository
Fundamentals in digital image processing#
Guillaume Witz
Licensed UNKNOWN
Tags: Bioimage Analysis, Include In Dalia
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, Include In Dalia
Content type: Notebook
Galaxy Training Material#
Licensed MIT
Tags: Exclude From Dalia
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: Bioimage Analysis, Include In Dalia
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: Bioimage Analysis, Include In Dalia
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, Include In Dalia
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, Include In Dalia
Content type: Notebook
IDC-Tutorials#
Andrey Fedorov, Daniela Schacherer, Dennis Bontempi, Bill Clifford, Vamsi Thiriveedhi, Brianna Major, wlongabaugh, dependabot[bot], Deepa Krishnaswamy
Published 2024-11-28T17:20:53+00:00
Licensed BSD-3-CLAUSE
Self-guided notebook tutorials to help get started with IDC
Tags: Bioimage Analysis, Include In Dalia
Content type: Github Repository
ITKElastix Examples#
Licensed APACHE-2.0
Tags: Bioimage Analysis, Exclude From Dalia
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, Include In Dalia
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, Include In Dalia
Content type: Notebook
Image analysis course material#
Christian Tischer
Licensed MIT
Training materials about image registration, big warp and elastix
Tags: Include In Dalia
Image processing for beginners#
Guillaume Witz
Licensed BSD-3-CLAUSE
Tags: Python, Bioimage Analysis, Include In Dalia
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, Include In Dalia
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, Include In Dalia
Content type: Book
ImageJ Macro Introduction#
Anna Klemm
Licensed UNKNOWN
Tags: Neubias, Imagej Macro, Bioimage Analysis, Include In Dalia
Content type: Slides, 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: Artificial Intelligence, Python, Include In Dalia
Content type: Notebook
Introduction to Image Analysis with Fiji#
Robert Haase, Benoit Lombardot
Licensed CC-BY-NC-4.0
Tags: Imagej, Fiji, Bioimage Analysis, Include In Dalia
Kreshuk Lab’s EMBL EIPP predoc course teaching material#
Adrian Wolny, Johannes Hugger, Qin Yu, Buglakova Alyona
Licensed UNKNOWN
Tags: Artificial Intelligence, Include In Dalia
Content type: Tutorial
LEO#
Rodrigo Escobar Diaz Guerrero
Published 2025-01-08T10:20:30+00:00
Licensed MIT
Linking Electronic Lab Notebooks and other sources with OMERO objects
Tags: OMERO, Research Data Management, Electronic Lab Notebooks, Exclude From Dalia
Content type: Github Repository
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, Exclude From Dalia
Content type: Github Repository, Slides, Notebook
MIDOG 2021#
Marc Aubreville, Frauke Wilm
Published 2021-03-16
Licensed UNLICENSED
Mitosis domain generation. Here you can find code of our own evaluations and a dockered reference algorithm for mitotic figures to use as a template.
Tags: Ai-Ready, Exclude From Dalia
Content type: Data
Machine Learning Workflow for Imaging Flow Cytometry (IFC)#
Licensed UNKNOWN
Tags: Cellprofiler, Bioimage Analysis, Include In Dalia
Content type: Tutorial
Materials for EMBL Coding Club Mini-Tutorials#
Jonas Hartmann, et al.
Licensed UNKNOWN
Tags: Python, Exclude From Dalia
Content type: Code, Notebook
Metabolic networks modelling with COBRApy#
Karin Sasaki, Aleksej Zelezniak
Licensed UNKNOWN
Tags: Python, Include In Dalia
Content type: Notebook
Models and Applications for BioImage.IO#
Wei Ouyang, et al.
Licensed UNKNOWN
Tags: Exclude From Dalia
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, Include In Dalia
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, Include In Dalia
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, Include In Dalia
Content type: Slides, 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, Include In Dalia
Content type: Slides, 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, Include In Dalia
Content type: Slides, 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, Include In Dalia
Content type: Slides, 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, Exclude From Dalia
Content type: Event, Publication, Documentation
NLP Course#
Yandex School of Data Analysis
Licensed MIT
YSDA course in Natural Language Processing
Tags: Natural Language Processing, Include In Dalia
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, Include In Dalia
Content type: Slides, Notebook
NeubiasPasteur2023_AdvancedCellPose#
Gaelle Letort
Licensed BSD-3-CLAUSE
Tutorial for running CellPose advanced functions
Tags: Bioimage Analysis, Artificial Intelligence, Include In Dalia
Content type: Github Repository
Nextflow Demo Pipelines for Image Processing#
Licensed UNKNOWN
Tags: Include In Dalia
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, Include In Dalia
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, Include In Dalia
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, Include In Dalia
Content type: Github Repository, Tutorial, Workshop, Slides
Omero Deployment examples#
Licensed BSD-2-CLAUSE
Tags: OMERO, Include In Dalia
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, Include In Dalia
Content type: Github Repository
Parallel_Fiji_Visualizer#
Matthew Mueller, Aaron, Advanced Bioimaging Center
Published 2024-05-15T06:14:24+00:00
Licensed BSD-3-CLAUSE
Tags: Fiji, Exclude From Dalia
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, Exclude From Dalia
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, Exclude From Dalia
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, Exclude From Dalia
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, Include In Dalia
Content type: Notebook
BiAPoL/PoL-BioImage-Analysis-TS-GPU-Accelerated-Image-Analysis
Predicting Axillary Lymph Node Metastasis in Early Breast Cancer Using Deep Learning on Primary Tumor Biopsy Slides#
Wenqi Tang, MIC Group
Published 2021-12-12
Licensed UNLICENSED
This repo is the official implementation of our paper “Predicting Axillary Lymph Node Metastasis in Early Breast Cancer Using Deep Learning on Primary Tumor Biopsy Slides”.
Tags: Ai-Ready, Exclude From Dalia
Content type: Data
Prompt-Engineering-LLMs-Course#
Isra Mekki
Published 2024-09-11T07:45:30+00:00
Licensed MIT
Tags: Llms, Prompt Engineering, Code Generation, Include In Dalia
Content type: Github Repository, Tutorial
HelmholtzAI-Consultants-Munich/Prompt-Engineering-LLMs-Course
PygamePrompts#
Lea Kabjesz, Lea Gihlein, Mara Lampert, FPGro
Published 2025-08-12T11:36:36+00:00
Licensed CC-BY-4.0
A collection of workshop materials for exploring prompting techniques by building a Snake game in Cursor.
Tags: Include In Dalia
Content type: Github Repository
Python BioImage Analysis Tutorial#
Jonas Hartmann
Licensed MIT
Tags: Python, Bioimage Analysis, Include In Dalia
Python Workshop - Image Processing#
Karin Sasaki, Jonas Hartmann
Licensed UNKNOWN
Tags: Python, Include In Dalia
Content type: Code, Notebook
Python for Microscopists#
Sreenivas Bhattiprolu
Licensed MIT
Tags: Python, Bioimage Analysis, Include In Dalia
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, Include In Dalia
Content type: Github Repository, Notebook, Collection
RDM4Mic Presentations#
Licensed CC-BY-4.0
Tags: Research Data Management, Exclude From Dalia
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, Exclude From Dalia
Content type: Github Repository
Scientific Visualization: Python + Matplotlib#
Nicolas P. Rougier
Licensed CC-BY-ND-SA-4.0
Tags: Python, Include In Dalia
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, Include In Dalia
Content type: Github Repository
Scripts_FilopodyanR - a case study for the NEUBIAS TS7 in Szeged#
Marion Louveaux
Licensed UNKNOWN
Tags: Neubias, Bioimage Analysis, Exclude From Dalia
Content type: Code
Setting up a remote desktop to use Napari in a browser#
Volker Hilsenstein
Licensed UNKNOWN
Tags: Include In Dalia
Content type: Tutorial
SimpleITK-Notebooks#
Ziv Yaniv et al.
Licensed APACHE-2.0
Jupyter notebooks for learning how to use SimpleITK
Tags: Bioimage Analysis, Simpleitk, Include In Dalia
Content type: Github Repository
Source Control Using Git and GitHub#
Licensed UNKNOWN
Tags: Include In Dalia
Content type: Tutorial
Statistical Rethinking#
Richard McElreath
Published 2024-03-01
Licensed CC0-1.0
This course teaches data analysis, but it focuses on scientific models. The unfortunate truth about data is that nothing much can be done with it, until we say what caused it. We will prioritize conceptual, causal models and precise questions about those models. We will use Bayesian data analysis to connect scientific models to evidence. And we will learn powerful computational tools for coping with high-dimension, imperfect data of the kind that biologists and social scientists face.
Tags: Statistics, Exclude From Dalia
Content type: Github Repository
Teaching Bioimage Analysis with Python#
Rafael Camacho
Licensed MIT
Tags: Python, Bioimage Analysis, Include In Dalia
Content type: Tutorial
Teaching ImageJ FIJI#
Rafael Camacho
Licensed MIT
Tags: Fiji, Bioimage Analysis, Include In Dalia
Content type: Tutorial
Training Deep Learning Models for Vision - Compact Course#
Constantin Pape, Adrian Wolny
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis, Include In Dalia
TrendsInMicroscopy2025#
Marcelo Zoccoler, Johannes Soltwedel
Published 2025-03-10T13:42:57+00:00
Licensed CC-BY-4.0
Course contents for biapol course at Trends in Microscopy conference 2025
Tags: Bioimage Analysis, Exclude From Dalia
Content type: Github Repository
Ultrack I2K 2024 Workshop Materials#
Jordão Bragantini, Teun Huijben
Licensed BSD3-CLAUSE
Tags: Bioimage Analysis, Include In Dalia
Content type: Workshop, Github Repository, Tutorial
V4SDB_Winter_School_2025#
Joanna Pylvänäinen
Published 2025-01-13T08:29:22+00:00
Training materials for V4SDB Student Winter School, 28th-31st January 2025 at ELTE Eötvös Loránd University in Budapest, Hungary
Tags: Cell Tracking, Bioimage Analysis, Exclude From Dalia
Content type: Github Repository, Collection
Virtual-I2K-2024-multiview-stitcher#
Marvin Albert
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, Include In Dalia
Content type: Github Repository, Tutorial
Workshop-June2024-Madrid#
Licensed MIT
Tags: Bioimage Analysis, Exclude From Dalia
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, Artifical Intelligence, Bioimage Analysis, Include In Dalia
Content type: Github Repository, Slides
ZEN & Python workshop#
Licensed GPL-3.0
Tags: Python, Napari, Bioimage Analysis, Include In Dalia
Content type: Collection, Notebook
ZIDAS 2020 Introduction to Deep Learning#
Estibaliz Gómez-de-Mariscal
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis, Include In Dalia
Content type: Slides
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
Tags: Bioimage Analysis, Exclude From Dalia
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, Exclude From Dalia
Content type: Application, Github Repository
bioimageio-chatbot#
Wei Ouyang, Wanlu Lei, Caterina Fuster-Barceló, Gabe Reder, arratemunoz, Weize, Curtis Rueden, Matt McCormick
Published 2023-10-10T16:05:49+00:00
Licensed MIT
Your Personal Assistant in Computational Bioimaging.
Tags: Artificial Intelligence, Bioimage Analysis, Exclude From Dalia
Content type: Github Repository
data_visualization_tutorial#
Stefan Halfpap
Published 2025-04-25T21:00:39+00:00
Tags: Data Visualization, Include In Dalia
Content type: Github Repository
datenbiene#
Torsten Stöter
Published 2025-02-02T18:50:20+00:00
Licensed GNU GENERAL PUBLIC LICENSE V3.0
Tags: Research Data Management, Exclude From Dalia
Content type: Github Repository, Software
dmtxSampleCreator#
SaibotMagd
Published 2023-06-06T11:52:14+00:00
Licensed APACHE-2.0
firefox extension: reads datamatrix code from camera and create a sample in an inventory to link it into an ELN.
Tags: Nfdi4Bioimage, Exclude From Dalia
Content type: Github Repository
embo-bia-2025#
Kevin Yamauchi
Published 2025-08-18T09:32:20+00:00
Licensed BSD-3-CLAUSE
Tags: Exclude From Dalia
Content type: Github Repository
i2k-2020-s3-zarr-workshop#
Constantin Pape, Christian Tischer
Licensed UNKNOWN
Tags: Python, Big Data, Exclude From Dalia
Content type: Github Repository
image-processing-basics#
Myles Scolnick
Published 2025-05-27T08:31:14+00:00
Licensed APACHE-2.0
Teaching material for image processing and analysis
Tags: Bioimage Analysis, Include In Dalia
Content type: Github Repository
imagequantification101#
Virginie, Guillaume Witz, Joel Lüthi
Published 2022-08-17T14:55:16+00:00
Licensed BSD-3-CLAUSE
Tags: Bioimage Analysis, Include In Dalia
Content type: Github Repository, Notebook, Collection
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, Include In Dalia
Content type: Github Repository, Tutorial
introduction-to-image-analysis#
Dave Barry, Stefania Marcotti, Sara Salgueiro Torres, Martin Jones, AlicjaSkorkowska
Published 2025-08-26T14:08:22+00:00
Licensed CC-BY-SA-4.0
Tags: Include In Dalia
Content type: Github Repository
napari-scipy2025-workshop#
Draga Doncila Pop
Published 2025-02-28T23:41:10+00:00
Licensed BSD-3-CLAUSE
This is a three-part workshop guiding you through using napari to view images, a brief bioimaging analysis application, and extending napari’s functionality with your own custom workflows.
Tags: Python, Napari, Include In Dalia
Content type: Github Repository
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, Include In Dalia
Content type: Github Repository, Tutorial
nextflow101#
Virginie
Published 2025-08-19T14:51:21+00:00
Licensed BSD-3-CLAUSE
NextFlow 101
Tags: Bioimage Analysis, Workflows, Include In Dalia
Content type: Github Repository
numpy pandas course#
Guillaume Witz
Licensed BSD-3-CLAUSE
Tags: Python, Include In Dalia
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: Exclude From Dalia
Content type: Github Repository, Application
ome2024-ngff-challenge#
Will Moore, Josh Moore, sherwoodf, jean-marie burel, Norman Rzepka, dependabot[bot], JensWendt, Joost de Folter, Torsten St\xF6ter, AybukeKY, Eric Perlman, Tom Boissonnet
Published 2024-08-30T12:00:53+00:00
Licensed BSD-3-CLAUSE
Project planning and material repository for the 2024 challenge to generate 1 PB of OME-Zarr data
Tags: Sharing, Nfdi4Bioimage, Research Data Management, Exclude From Dalia
Content type: Github Repository
omero-arc#
Christoph Moehl, Peter Zentis, Niraj Kandpal
Published 2023-12-18T16:11:04+00:00
Licensed GNU GENERAL PUBLIC LICENSE V3.0
Library to export OMERO projects to ARC repositories
Tags: OMERO, Research Data Management, Exclude From Dalia
Content type: Github Repository, Software
omero-ontop-mappings#
Carsten Fortmann-Grote, andrawaag, Jerven Bolleman
Published 2024-09-13T08:01:09+00:00
ONTOP module for querying OMERO with SPARQL
Tags: OMERO, Exclude From Dalia
Content type: Github Repository
omero-vitessce#
Michele Bortolomeazzi
Published 2024-11-25T10:51:01+00:00
Licensed AGPL-3.0
OMERO.web plugin for the Vitessce multimodal data viewer.
Tags: OMERO, Exclude From Dalia
Content type: Github Repository
patho_prompt_injection#
JanClusmann, Tim Lenz
Published 2024-11-08T08:32:03+00:00
Licensed GPL-3.0
Tags: Histopathology, Bioimage Analysis, Exclude From Dalia
Content type: Github Repository, Notebook
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, Exclude From Dalia
Content type: Code
qupath-workshop#
Antoine A. Ruzette, dependabot[bot]
Published 2025-01-16T14:05:02+00:00
Licensed CC-BY-4.0
Materials supporting the QuPath workshop at Harvard Medical School.
Tags: Notebook, Slides, Collection, Include In Dalia
Content type: Github Repository
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, Exclude From Dalia
Content type: Application, Github Repository
rse-skills-workshop#
Jack Atkinson
Published 2023-12-22T17:39:48+00:00
Licensed GPL-3.0
Teaching materials for improving research software writing abilities.
Tags: Research Software Engineering, Include In Dalia
Content type: Github Repository, Slides
scanpy-tutorials#
Alex Wolf, pre-commit-ci[bot], Philipp A., Isaac Virshup, Ilan Gold, Giovanni Palla, Fidel Ramirez, G\xF6k\xE7en Eraslan, Sergei Rybakov, Abolfazl (Abe), Adam Gayoso, Dinesh Palli, Gregor Sturm, Jan Lause, Karin Hrovatin, Krzysztof Polanski, RaphaelBuzzi, Yimin Zheng, Yishen Miao, evanbiederstedt
Published 2018-12-16T03:42:46+00:00
Licensed BSD-3-CLAUSE
Scanpy Tutorials.
Tags: Single-Cell Analysis, Bioimage Analysis, Include In Dalia
Content type: 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, Include In Dalia
Content type: Github Repository
shapeanalysis101#
Virginie, Johannes Hugger
Published 2021-05-17T13:32:40+00:00
Licensed BSD-3-CLAUSE
A tutorial of classical shape analysis methods
Tags: Bioimage Analysis, Include In Dalia
Content type: Github Repository, Notebook, Collection
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, Include In Dalia
Content type: Github Repository
training#
Erick Martins Ratamero, dependabot[bot]
Published 2020-03-09T13:25:54+00:00
Licensed MIT
repo for training materials
Tags: Exclude From Dalia
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, Include In Dalia
Content type: Github Repository