Notebook (47)#
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
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
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
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
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
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