Github.com (113)#

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

https://doi.org/10.1017/s2633903x21000039

ciminilab/2021_Jamali_BiologicalImaging


2022 MIC Workshop on Bioimage processing with Python#

Guillaume Witz

Licensed UNKNOWN

Tags: Python, Bioimage Analysis

Content type: Notebook

guiwitz/MICPy_Workshop_2022


Adding a Workflow to BIAFLOWS#

Sébastien Tosi, Volker Baecker, Benjamin Pavie

Licensed BSD-2-CLAUSE

Tags: Neubias, Bioimage Analysis

Content type: Slide

RoccoDAnt/Defragmentation_TrainingSchool_EOSC-Life_2022


Analysis of High-Throughput Microscopy Image Data#

Kota Miura, Christoph Schiklenk, Clemens Lakner, Christian Tischer, Aliaksandr Halavatyi

Published 2014

Licensed UNKNOWN

miura/HTManalysisCourse


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

ScaDS/BIDS-lecture-2024


Basics of Image Processing and Analysis#

Kota Miura

Licensed ALL RIGHTS RESERVED

Tags: Bioimage Analysis

Content type: Book

miura/ij_textbook1


Bio Image Analysis#

Christian Tischer

Licensed UNKNOWN

Tags: Bioimage Analysis

Content type: Slide

tischi/presentation-image-analysis


Bio-image Analysis ICOB 2023#

Tags: Bioimage Analysis

Content type: Workshop, Collection

WeiChenChu/Bioimage_Analysis_ICOB_2023


Bio-image Analysis Workshop Kioto and Taipei 23/24#

Tags: Bioimage Analysis

Content type: Workshop, Collection

Koushouu/Bioimage-Analysis-Workshop-23-24


Bio-image Analysis Workshop Taipei#

Tags: Bioimage Analysis

Content type: Workshop, Collection

Koushouu/Bioimage-Analysis-Workshop-Taipei


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

ScaDS/BIDS-lecture-2024


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

BiAPoL/Bio-image_Analysis_with_Python


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

NL-BioImaging/biomero


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

https://www.biorxiv.org/content/10.1101/2023.06.05.543701v1

COBA-NIH/2023_ImageAnalysisSurvey


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


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


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

CellProfiler/tutorials


CellTrackColab#

Guillaume Jacquemet

Licensed MIT

Content type: Notebook, Collection

https://www.biorxiv.org/content/10.1101/2023.10.20.563252v2

guijacquemet/CellTracksColab


Collection of teaching material for deep learning for (biomedical) image analysis#

Constantin Pape

Licensed MIT

Tags: Artificial Intelligence, Bioimage Analysis

constantinpape/dl-teaching-resources


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


DL4MicEverywhere#

Iván Hidalgo, et al.

Licensed CC-BY-4.0

Content type: Notebook, Collection

HenriquesLab/DL4MicEverywhere


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 Based Segmentation For Biologists#

Licensed AGPL-3.0

Tags: Python, R, Artificial Intelligence

Content type: Notebook

tpecot/DeepLearningBasedSegmentationForBiologists


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


Deep Vision and Graphics#

Victor Yurchenko, Fedor Ratnikov, Viktoriia Checkalina

Licensed MIT

Tags: Python, Artificial Intelligence

Content type: Notebook

yandexdataschool/deep_vision_and_graphics


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

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


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

juglab/EmbedSeg


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


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/

timmonko/napari-ndev


Fundamentals in digital image processing#

Guillaume Witz

Licensed UNKNOWN

Tags: Bioimage Analysis

Content type: Notebook

guiwitz/Fundamentals_image_processing


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

jni/halfway-to-i2k-skimage-napari


Galaxy Training Material#

Licensed MIT

Content type: Slides, Tutorial

galaxyproject/training-material


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

StRigaud/clesperanto_workshop_I2K24


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

https://saalfeldlab.github.io/i2k2024-lazy-workshop/

saalfeldlab/i2k2024-lazy-workshop


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

haesleinhuepf/i2k2024-ai-code-generation


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

RMS-DAIM/Python-for-Bioimage-Analysis


ITKElastix Examples#

Licensed APACHE-2.0

Tags: Bioimage Analysis

InsightSoftwareConsortium/ITKElastix


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

https://datacarpentry.org/image-processing/

datacarpentry/image-processing


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

scipy-2023-image-analysis/tutorial


Image analysis course material#

Christian Tischer

Licensed MIT

Training materials about image registration, big warp and elastix

tischi/image-analysis-course-material


Image processing for beginners#

Guillaume Witz

Licensed BSD-3-CLAUSE

Tags: Python, Bioimage Analysis

Content type: Notebook

guiwitz/PyImageCourse_beginner


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

guiwitz/Python_image_processing


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

cytomining/profiling-handbook

https://cytomining.github.io/profiling-handbook/


ImageJ Macro Introduction#

Anna Klemm

Licensed UNKNOWN

Tags: Neubias, Imagej Macro, Bioimage Analysis

Content type: Slide, Code

ahklemm/ImageJMacro_Introduction


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

computational-cell-analytics/dl-for-micro


Introduction to Image Analysis with Fiji#

Robert Haase, Benoit Lombardot

Licensed CC-BY-NC-4.0

Tags: Imagej, Fiji, Bioimage Analysis

mpicbg-scicomp/CourseIntroToIA


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


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

deeplife4eu/Lecture-materials


Machine Learning Workflow for Imaging Flow Cytometry (IFC)#

Licensed UNKNOWN

Tags: Cellprofiler, Bioimage Analysis

Content type: Tutorial

holgerhennig/machine-learning-IFC


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


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

guiwitz/neubias_academy_biapy


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


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

NFDI4BIOIMAGE/Cologne-Hackathon-2023

https://doi.org/10.5281/zenodo.10609770


NLP Course#

Yandex School of Data Analysis

Licensed MIT

YSDA course in Natural Language Processing

Tags: Natural Language Processing

Content type: Github Repository

yandexdataschool/nlp_course


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


NeubiasPasteur2023_AdvancedCellPose#

Gaelle Letort

Licensed BSD-3-CLAUSE

Tutorial for running CellPose advanced functions

Tags: Cellpose, Segmentation

Content type: Github Repository

gletort/NeubiasPasteur2023_AdvancedCellPose


Nextflow Demo Pipelines for Image Processing#

Licensed UNKNOWN

Content type: Code

JaneliaSciComp/nf-demos


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

rmassei/2024-jn-omero-pipeline


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

dwaithe/ONBI_image_analysis


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

CellMigrationLab/I2K_2024


Omero Deployment examples#

Licensed BSD-2-CLAUSE

Tags: OMERO

Content type: Collection

ome/omero-deployment-examples


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

GReD-Clermont/omero_batch-plugin


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

ome/omero-cli-transfer


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

GReD-Clermont/simple-omero-client


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

WhoIsJack/python-bioimage-analysis-tutorial


Python Workshop - Image Processing#

Karin Sasaki, Jonas Hartmann

Licensed UNKNOWN

Tags: Python

Content type: Code, Notebook

karinsasaki/python-workshop-image-processing


Python for Microscopists#

Sreenivas Bhattiprolu

Licensed MIT

Tags: Python, Bioimage Analysis

Content type: Notebook, Collection

bnsreenu/python_for_microscopists


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

qupath/i2k-qupath-for-python-programmers


RDM4Mic Presentations#

Licensed CC-BY-4.0

Tags: Research Data Management

Content type: Collection

German-BioImaging/RDM4mic


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

SaibotMagd/RDM_system_connector


Scientific Visualization: Python + Matplotlib#

Nicolas P. Rougier

Licensed CC-BY-ND-SA-4.0

Tags: Python

Content type: Book

rougier/scientific-visualization-book

https://inria.hal.science/hal-03427242/document


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

scipy/scipy-cookbook


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 remote desktop to use Napari in a browser#

Volker Hilsenstein

Licensed UNKNOWN

Content type: Tutorial

VolkerH/Jupyter-Napari-Desktop


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

InsightSoftwareConsortium/SimpleITK-Notebooks


Source Control Using Git and GitHub#

Licensed UNKNOWN

Content type: Tutorial

JaneliaSciComp/2020AprilGitCourse


Teaching Bioimage Analysis with Python#

Rafael Camacho

Licensed MIT

Tags: Python, Bioimage Analysis

Content type: Tutorial

CamachoDejay/teaching-bioimage-analysis-python


Teaching ImageJ FIJI#

Rafael Camacho

Licensed MIT

Tags: Fiji, Bioimage Analysis

Content type: Tutorial

CamachoDejay/Teaching-ImageJ-FIJI


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


Ultrack I2K 2024 Workshop Materials#

Jordão Bragantini, Teun Huijben

Licensed BSD3-CLAUSE

Tags: Segmentation, Bioimage Analysis, Training

Content type: Workshop, Github Repository, Tutorial

royerlab/ultrack-i2k2024

https://royerlab.github.io/ultrack-i2k2024/


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

m-albert/Virtual-I2K-2024-multiview-stitcher


Workshop-June2024-Madrid#

Licensed MIT

Tags: Bioimage Analysis

Content type: Workshop, Collection

bioimage-io/Workshop-June2024-Madrid


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

rmassei/ymia_python_event_series_material


ZEN & Python workshop#

Licensed GPL-3.0

Tags: Python, Napari, Bioimage Analysis

Content type: Collection, Notebook

zeissmicroscopy/ZEN_Python_OAD_workshop


ZIDAS 2020 Introduction to Deep Learning#

Estibaliz Gómez-de-Mariscal

Licensed UNKNOWN

Tags: Artificial Intelligence, Bioimage Analysis

Content type: Slide

esgomezm/zidas2020_intro_DL


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

HenriquesLab/ZeroCostDL4Mic

https://www.nature.com/articles/s41467-021-22518-0

https://doi.org/10.1038/s41467-021-22518-0


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

glencoesoftware/bioformats2raw


i2k-2020-s3-zarr-workshop#

Constantin Pape, Christian Tischer

Licensed UNKNOWN

Tags: Python, Big Data

Content type: Github Repository

tischi/i2k-2020-s3-zarr-workshop


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

vibbits/introduction-to-generative-ai

https://liascript.github.io/course/?https://raw.githubusercontent.com/vibbits/introduction-to-generative-ai/refs/heads/main/README.md


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

vibbits/nextflow-workshop

https://liascript.github.io/course/?https://raw.githubusercontent.com/vibbits/nextflow-workshop/main/README.md#1


numpy pandas course#

Guillaume Witz

Licensed BSD-3-CLAUSE

Tags: Python

Content type: Notebook

guiwitz/NumpyPandas_course


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

https://ome.github.io/ome-ngff-validator/

ome/ome-ngff-validator


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

quantixed/TheDigitalCell

https://zenodo.org/records/2643411

https://doi.org/10.5281/zenodo.2643411


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

glencoesoftware/raw2ometiff


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

INRIA/scikit-learn-mooc


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

scikit-image/skimage-tutorials


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

NEUBIAS/training-resources