Notebook (54)#
2022 MIC Workshop on Bioimage processing with Python#
Guillaume Witz
Licensed UNKNOWN
Tags: Python, Bioimage Analysis
Content type: Notebook
A Fiji Scripting Tutorial#
Albert Cardona
Licensed CC0-1.0
Tags: Imagej, Bioimage Analysis
Content type: Notebook
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
BioImage Analysis Notebooks#
Robert Haase et al.
Licensed [‘CC-BY-4.0’, ‘BSD-3-CLAUSE’]
Tags: Python, Bioimage Analysis
Content type: Book, Notebook
https://haesleinhuepf.github.io/BioImageAnalysisNotebooks/intro.html
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 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
Community-developed checklists for publishing images and image analyses#
Beth Cimini et al.
Licensed BSD LICENSE
This book is a companion to the Nature Methods publication Community-developed checklists for publishing images and image analyses. In this paper, members of QUAREP-LiMi have proposed 3 sets of standards for publishing image figures and image analysis - minimal requirements, recommended additions, and ideal comprehensive goals. By following this guidance, we hope to remove some of the stress non-experts may face in determining what they need to do, and we also believe that researchers will find their science more interpretable and more reproducible.
Tags: Bioimage Analysis, Research Data Management
Content type: Notebook, Collection
https://quarep-limi.github.io/WG12_checklists_for_image_publishing/intro.html
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
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
Elastix tutorial#
Marvin Albert
Licensed BSD LICENSE
Tutorial material for teaching the basics of (itk-)elastix for image registration in microscopy images.
Tags: Image Registration, Itk, Elastix
Content type: Notebook, Collection
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
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
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 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
Introduction to Bioimage Analysis#
Pete Bankhead
Licensed CC-BY-4.0
Tags: Python, Imagej, Bioimage Analysis
Content type: Book, Notebook
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
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
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
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 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
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
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
Open Image Data Handbook#
Kevin Yamauchi
Licensed CC-BY-4.0
Tags: Neubias, Research Data Management, Napari, Python, Bioimage Analysis
Content type: Book, Notebook
PoL Bio-Image Analysis Early Career Bio-image Analysis Training School#
Tags: Bioimage Analysis, Python
Content type: Event, Notebook
https://biapol.github.io/PoL-BioImage-Analysis-TS-Early-Career-Track/intro.html
PoL Bio-Image Analysis GPU Accelerated Image Analysis Training School#
Tags: Bioimage Analysis, Python
Content type: Event, Notebook
https://biapol.github.io/PoL-BioImage-Analysis-TS-GPU-Accelerated-Image-Analysis/intro.html
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
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
QI 2024 Analysis Lab Manual#
Beth Cimini, Florian Jug, QI 2024
Licensed CC-BY-4.0
This book contains the quantitative analysis labs for the QI CSHL course, 2024
Tags: Segmentation, Python
Content type: Notebook
https://bethac07.github.io/qi_2024_analysis_lab_manual/intro.html
QM Course Lectures on Bio-Image Analysis with napari 2024#
Marcelo Leomil Zoccoler
Licensed CC-BY-4.0
In these lectures, we will explore ways to analyze microscopy images with Python and visualize them with napari, an nD viewer open-source software. The analysis will be done in Python mostly using the scikit-image, pyclesperanto and apoc libraries, via Jupyter notebooks. We will also explore some napari plugins as an interactive and convenient alternative way of performing these analysis, especially the napari-assistant, napari-apoc and napari-flim-phasor-plotter plugins.
Tags: Napari, Python
Content type: Notebook
https://zoccoler.github.io/QM_Course_Bio_Image_Analysis_with_napari_2024
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
ZEN & Python workshop#
Licensed GPL-3.0
Tags: Python, Napari, Bioimage Analysis
Content type: Collection, Notebook
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
numpy pandas course#
Guillaume Witz
Licensed BSD-3-CLAUSE
Tags: Python
Content type: Notebook