Merge branch 'main' of https://github.com/NFDI4BIOIMAGE/training

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
   authors: Marcelo Zoccoler
   type: blog
@@ -19,6 +17,8 @@ resources:
 - name: Getting started with Mambaforge and Python
   type: blog
   authors: 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
@@ -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/

resources/materials.yml

@@ -12,18 +12,25 @@ resources:
   type:
   - collection
   - notebook
+  tags:
+  - python
   url: https://haesleinhuepf.github.io/BioImageAnalysisNotebooks/intro.html
 
 - name: Introduction to Bioimage Analysis
   authors: Pete Bankhead
   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
@@ -108,87 +115,117 @@ 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
   type:
   - 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
   type:
   - collection
   - notebook
   license: GPL-3.0
+  tags:
+  - python
+  - napari
   url: https://github.com/zeissmicroscopy/ZEN_Python_OAD_workshop
 
 - name: Research Data Management Seminar - Slides
   authors: Della Chiesa, Stefano
   url: https://zenodo.org/record/6602101
-  type: 
+  type:
   - collection
   - slide
 
@@ -201,7 +238,7 @@ resources:
   type: 
   - collection
   - publication
-  url: 
+  url:
   - https://doi.org/10.1371/journal.pbio.3002167
   - https://www.bioimagingguide.org/
 
@@ -210,7 +247,7 @@ resources:
   type:
   - collection
   - data
-  url: 
+  url:
   - https://www.nature.com/articles/nmeth.2083
   - https://bbbc.broadinstitute.org/
   description: Broad Bioimage Benchmark Collection (BBBC)

resources/workflow-tools.yml

@@ -7,51 +7,58 @@ resources:
   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
   authors: Birgit Möller, Markus Glaß, Danny Misiak, Stefan Posch
   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"
   authors: 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"
   authors: Stephen J. Cross, Jordan D. J. R. Fisher, Mark A. Jepson
@@ -60,11 +67,12 @@ resources:
   - 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
 

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()
+    main()