Bsd-3-clause (26)#
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
A biologist’s guide to planning and performing quantitative bioimaging experiments#
Rebecca A. Senft, Barbara Diaz-Rohrer, Pina Colarusso, Lucy Swift, Nasim Jamali, Helena Jambor, Thomas Pengo, Craig Brideau, Paula Montero Llopis, Virginie Uhlmann, Jason Kirk, Kevin Andrew Gonzales, Peter Bankhead, Edward L. Evans III, Kevin W. Eliceiri, Beth A. Cimini
Licensed BSD-3-CLAUSE
Content type: Collection, Publication
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
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
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
Community-developed checklists for publishing images and image analyses#
Beth Cimini et al.
Licensed BSD-3-CLAUSE
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
Elastix tutorial#
Marvin Albert
Licensed BSD-3-CLAUSE
Tutorial material for teaching the basics of (itk-)elastix for image registration in microscopy images.
Tags: Image Registration, Itk, Elastix
Content type: Notebook, Collection
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
Content type: Documentation, Github Repository, Tutorial
https://timmonko.github.io/napari-ndev/tutorial/01_example_pipeline/
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: Bioimage Analysis
Content type: Github Repository, Workshop, Tutorial, Notebook
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
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
ImageJ2 API-beating#
Robert Haase
Licensed BSD-3-CLAUSE
Tags: Neubias, Imagej, Bioimage Analysis
Content type: Slides
Multi-view fusion#
Robert Haase
Licensed BSD-3-CLAUSE
Lecture slides of a session on Multiview Fusion in Fiji
Tags: Neubias, Imagej, Bioimage Analysis
Content type: Slides
https://git.mpi-cbg.de/rhaase/lecture_multiview_registration
NEUBIAS Academy @HOME: Interactive Bioimage Analysis with Python and Jupyter#
Licensed BSD-3-CLAUSE
Tags: Python, Neubias, Bioimage Analysis
Content type: Notebook
NeubiasPasteur2023_AdvancedCellPose#
Gaelle Letort
Licensed BSD-3-CLAUSE
Tutorial for running CellPose advanced functions
Tags: Bioimage Analysis, Artificial Intelligence
Content type: Github Repository
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
Tracking Theory, TrackMate, and Mastodon#
Robert Haase
Licensed BSD-3-CLAUSE
Lecture slides of a session on Cell Tracking in Fiji
Tags: Neubias, Imagej, Bioimage Analysis
Content type: Slides
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
WorkflowHub#
Stian Soiland-Reyes, Finn Bacall, Bert Droesbeke, Alan R Williams, Johan Gustafsson, et al.
Licensed BSD-3-CLAUSE
A registry for describing, sharing and publishing scientific computational workflows.
Tags: Bioinformatics, Workflow, Workflow Engine, Python, R
Content type: Collection
Working with objects in 2D and 3D#
Robert Haase
Licensed BSD-3-CLAUSE
Tags: Neubias, Imagej, Bioimage Analysis
Content type: Slides
https://git.mpi-cbg.de/rhaase/lecture_working_with_objects_in_2d_and_3d
Working with pixels#
Robert Haase
Licensed BSD-3-CLAUSE
Tags: Neubias, Imagej, Bioimage Analysis
Content type: Slides
numpy pandas course#
Guillaume Witz
Licensed BSD-3-CLAUSE
Tags: Python
Content type: Notebook
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
Content type: Github Repository
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
Content type: Github Repository