Napari (13)#
Annotating 3D images in napari#
Mara Lampert
Tags: Python, Napari, Bioimage Analysis
Content type: Blog
https://focalplane.biologists.com/2023/03/30/annotating-3d-images-in-napari/
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 with Napari#
Fabrizio Musacchio
Licensed CC-BY-ND-SA-4.0
Tags: Python, Napari, Bioimage Analysis
Content type: Collection
https://www.fabriziomusacchio.com/teaching/teaching_bioimage_analysis/
Chris Halvin YouTube channel#
Licensed UNKNOWN
Tags: Napari, Python, Bioimage Analysis
Content type: Collection, Video
https://www.youtube.com/@chrishavlin
https://www.youtube.com/playlist?list=PLqbhAmYZU5KxuAcnNBIxyBkivUEiKswq1
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/
Feature extraction in napari#
Mara Lampert
Tags: Python, Napari, Bioimage Analysis
Content type: Blog
https://focalplane.biologists.com/2023/05/03/feature-extraction-in-napari/
Intro napari slides#
Peter Sobolewski
Licensed MIT
Introduction to napari workshop run at JAX (Spring 2024).
Tags: Napari
Content type: Slides
https://thejacksonlaboratory.github.io/intro-napari-slides/#/section
Open Image Data Handbook#
Kevin Yamauchi
Licensed CC-BY-4.0
Tags: Neubias, Research Data Management, Napari, Python, Bioimage Analysis
Content type: Book, Notebook
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
Quality assurance of segmentation results#
Mara Lampert
Tags: Python, Napari, Bioimage Analysis
Content type: Blog
https://focalplane.biologists.com/2023/04/13/quality-assurance-of-segmentation-results/
Rescaling images and pixel (an)isotropy#
Mara Lampert
Tags: Python, Napari, Bioimage Analysis
Content type: Blog
https://focalplane.biologists.com/2023/03/02/rescaling-images-and-pixel-anisotropy/
Tracking in napari#
Mara Lampert
Tags: Python, Napari, Bioimage Analysis
Content type: Blog
https://focalplane.biologists.com/2023/06/01/tracking-in-napari/
ZEN & Python workshop#
Licensed GPL-3.0
Tags: Python, Napari, Bioimage Analysis
Content type: Collection, Notebook
zeissmicroscopy/ZEN_Python_OAD_workshop