From 927cb25a0e274b3fcfd1779020f83907f639dc06 Mon Sep 17 00:00:00 2001 From: clement Date: Tue, 10 Oct 2023 12:06:36 +0200 Subject: [PATCH 1/3] add tags when possible --- resources/blog_posts.yml | 4 +-- resources/materials.yml | 47 ++++++++++++++++++++++++++++++++---- resources/workflow-tools.yml | 40 ++++++++++++++++++------------ 3 files changed, 69 insertions(+), 22 deletions(-) diff --git a/resources/blog_posts.yml b/resources/blog_posts.yml index e26b48f..1b2835d 100644 --- a/resources/blog_posts.yml +++ b/resources/blog_posts.yml @@ -4,8 +4,6 @@ resources: type: blog url: https://focalplane.biologists.com/2023/07/26/sharing-your-poster-on-figshare/ - - - name: Running Deep-Learning Scripts in the BiA-PoL Omero Server author: Marcelo Zoccoler type: blog @@ -19,6 +17,8 @@ resources: - name: Getting started with Mambaforge and Python type: blog author: Mara Lampert + tags: + - python url: https://biapol.github.io/blog/mara_lampert/getting_started_with_mambaforge_and_python/readme.html - name: Promoting Data Management at the Nikon Imaging Center and Cell Biology Microscopy Facility diff --git a/resources/materials.yml b/resources/materials.yml index 29038ec..990b807 100644 --- a/resources/materials.yml +++ b/resources/materials.yml @@ -12,6 +12,8 @@ resources: type: - collection - notebook + tags: + - python url: https://haesleinhuepf.github.io/BioImageAnalysisNotebooks/intro.html - name: Introduction to Bioimage Analysis @@ -19,11 +21,16 @@ resources: type: - collection - notebook + tags: + - python + - imagej url: https://bioimagebook.github.io/index.html - name: Generative artificial intelligence for bio-image analysis authors: Robert Haase type: slide + tags: + - python url: https://f1000research.com/slides/12-971 - name: MicroscopyDB @@ -108,54 +115,72 @@ resources: - notebook license: BSD 3-Clause url: https://github.com/CellProfiler/tutorials + description: CellProfiler tutorials and guided exercises about translocation, segmentation, pixel-based classification and quality control - name: ONBI image analysis type: - collection - notebook license: GPL-2.0 + tags: + - python url: https://github.com/dwaithe/ONBI_image_analysis + description: "This repository contains the materials for the University of Oxford DTC ONBI Image Analysis course." - name: A Fiji Scripting Tutorial type: - collection license: Public_domain + tags: + - imagej url: https://syn.mrc-lmb.cam.ac.uk/acardona/fiji-tutorial/ - name: Lecture Applied Bioimage Analysis type: - collection - slide + tags: + - imagej url: https://git.mpi-cbg.de/rhaase/lecture_applied_bioimage_analysis - name: ImageJ API-beating type: - slide license: BSD 3-Clause + tags: + - imagej url: https://git.mpi-cbg.de/rhaase/lecture_imagej2_dev - name: Multi-view fusion type: - slide license: BSD 3-Clause + tags: + - imagej url: https://git.mpi-cbg.de/rhaase/lecture_multiview_registration - name: Tracking Theory, TrackMate, and Mastodon type: - slide license: BSD 3-Clause + tags: + - imagej url: https://git.mpi-cbg.de/rhaase/lecture_tracking_trackmate - name: Working with pixels type: - slide license: BSD 3-Clause + tags: + - imagej url: https://git.mpi-cbg.de/rhaase/lecture_working_with_pixels - name: Working with objects in 2D and 3D type: - slide license: BSD 3-Clause + tags: + - imagej url: https://git.mpi-cbg.de/rhaase/lecture_working_with_objects_in_2d_and_3d - name: Image processing with Python @@ -163,19 +188,28 @@ resources: - collection - notebook license: MIT + tags: + - python url: https://github.com/guiwitz/Python_image_processing + description: "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." - name: Deep Learning Based Segmentation For Biologists type: - collection - notebook license: AGPL-3.0 license + tags: + - python + - R url: https://github.com/tpecot/DeepLearningBasedSegmentationForBiologists/tree/main - name: Bioimage analysis with Napari type: - collection license: CC BY-NC-SA 4.0 + tags: + - python + - napari url: https://www.fabriziomusacchio.com/teaching/teaching_bioimage_analysis/#syllabus - name: ZEN & Python workshop @@ -183,12 +217,15 @@ resources: - collection - notebook license: GPL-3.0 + tags: + - python + - napari url: https://github.com/zeissmicroscopy/ZEN_Python_OAD_workshop - name: Research Data Management Seminar - Slides author: Della Chiesa, Stefano url: https://zenodo.org/record/6602101 - type: + type: - collection - slide @@ -198,19 +235,19 @@ resources: - name: A biologist’s guide to planning and performing quantitative bioimaging experiments author: 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 - type: + type: - collection - publication - url: + url: - https://doi.org/10.1371/journal.pbio.3002167 - https://www.bioimagingguide.org/ - name: Annotated high-throughput microscopy image sets for validation - author: Vebjorn Ljosa, Katherine L Sokolnicki, Anne E Carpenter + author: Vebjorn Ljosa, Katherine L Sokolnicki, Anne E Carpenter type: - collection - data - url: + url: - https://www.nature.com/articles/nmeth.2083 - https://bbbc.broadinstitute.org/ description: Broad Bioimage Benchmark Collection (BBBC) diff --git a/resources/workflow-tools.yml b/resources/workflow-tools.yml index b603dd9..6ddee66 100644 --- a/resources/workflow-tools.yml +++ b/resources/workflow-tools.yml @@ -1,70 +1,78 @@ resources: - name: "JIPipe: visual batch processing for ImageJ" author: Ruman Gerst, Zoltán Cseresnyés & Marc Thilo Figge - type: + type: - publication - documentation url: - https://www.nature.com/articles/s41592-022-01744-4 - https://jipipe.hki-jena.de/ - tags: + tags: - NFDI4BioImage - workflow engine + - imagej description: JIPipe is an open-source visual programming language for easy-access pipeline development - + - name: MiToBo - A Toolbox for Image Processing and Analysis author: Birgit Möller, Markus Glaß, Danny Misiak, Stefan Posch - type: + type: - publication - documentation - url: + url: - https://openresearchsoftware.metajnl.com/articles/10.5334/jors.103 - https://mitobo.informatik.uni-halle.de/ - tags: + tags: - workflow engine + - imagej description: The Microscope Image Analysis Toolbox is a toolbox with a collection of algorithms for processing and analyzing digital images. - name: "BiaPy: Bioimage analysis pipelines in Python" author: Daniel Franco-Barranco et al type: documentation url: https://biapy.readthedocs.io/ + tags: + - python description: BiaPy is an open source Python library for building bioimage analysis pipelines, also called workflows. - name: Galaxy Documentation type: documentation url: https://usegalaxy.org/ - tags: + tags: - workflow engine description: Galaxy is an open source, web-based platform for data intensive biomedical research. - name: Fractal Documentation type: documentation url: https://fractal-analytics-platform.github.io/ - tags: + tags: - workflow engine + - python + - napari description: Fractal is a framework to process high-content imaging data at scale and prepare it for interactive visualization. - + - name: Snakemake Documentation type: documentation - url: + url: - https://snakemake.readthedocs.io/en/stable/ - https://academic.oup.com/bioinformatics/article/28/19/2520/290322 - tags: + tags: - workflow engine - description: The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. + - python + description: The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. - name: "ModularImageAnalysis (MIA): Assembly of modularisedimage and object analysis workflows in ImageJ" author: Stephen J. Cross, Jordan D. J. R. Fisher, Mark A. Jepson - type: + type: - publication - documentation tags: - workflow engine - url: + - imagej + url: - https://doi.org/10.1111/jmi.13227 - https://mianalysis.github.io/ description: ModularImageAnalysis is a Fiji plugin providing a modular framework for assembling image and object analysis workflows - + - name: NextFlow documentation type: documentation url: https://www.nextflow.io/ @@ -75,5 +83,7 @@ resources: - name: NextFlow core type: collection url: https://nf-co.re/ + tags: + - python description: nf-core is a community effort to collect a curated set of analysis pipelines built using Nextflow From 720377e718c630f6ea89a10c0967ec93c6fef320 Mon Sep 17 00:00:00 2001 From: clement Date: Tue, 10 Oct 2023 12:33:34 +0200 Subject: [PATCH 2/3] add blog --- resources/blog_posts.yml | 46 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/resources/blog_posts.yml b/resources/blog_posts.yml index 1b2835d..0ea53b2 100644 --- a/resources/blog_posts.yml +++ b/resources/blog_posts.yml @@ -31,3 +31,49 @@ resources: type: blog url: https://blog.delmic.com/data-handling-in-large-scale-electron-microscopy +- name: Tracking in napari + type: blog + author: Mara Lampert + tags: + - python + - napari + url: https://focalplane.biologists.com/2023/06/01/tracking-in-napari/ + +- name: Feature extraction in napari + type: blog + author: Mara Lampert + tags: + - python + - napari + url: https://focalplane.biologists.com/2023/05/03/feature-extraction-in-napari/ + +- name: Annotating 3D images in napari + type: blog + author: Mara Lampert + tags: + - python + - napari + url: https://focalplane.biologists.com/2023/03/30/annotating-3d-images-in-napari/ + +- name: Annotating 3D images in napari + type: blog + author: Robert Haase + tags: + - python + url: https://focalplane.biologists.com/2022/12/08/managing-scientific-python-environments-using-conda-mamba-and-friends/ + +- name: Quality assurance of segmentation results + type: blog + author: Mara Lampert + tags: + - python + - napari + url: https://focalplane.biologists.com/2023/04/13/quality-assurance-of-segmentation-results/ + +- name: Rescaling images and pixel (an)isotropy + type: blog + author: Mara Lampert + tags: + - python + - napari + url: https://focalplane.biologists.com/2023/03/02/rescaling-images-and-pixel-anisotropy/ From 57c2e2835d7075e6211bb0a456d60b9d52d07711 Mon Sep 17 00:00:00 2001 From: Robert Haase Date: Tue, 10 Oct 2023 19:41:10 +0200 Subject: [PATCH 3/3] fix typo in code closes #17 --- scripts/generate_link_lists.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scripts/generate_link_lists.py b/scripts/generate_link_lists.py index d8b2de7..7bca20f 100644 --- a/scripts/generate_link_lists.py +++ b/scripts/generate_link_lists.py @@ -85,11 +85,11 @@ def write_md(resources, content_type_name, filename): url = properties['url'] if type(url) is list: for u in url: - file.write(f"\n[{u}]{u})\n") + file.write(f"\n[{u}]({u})\n") else: file.write(f"\n[{url}]({url})\n") file.write(f"\n") if __name__ == "__main__": - main() \ No newline at end of file + main()