Merge pull request #64 from ClementCaporal/more-resources

More resources

resources/materials.yml

@@ -1224,7 +1224,7 @@ resources:
   - notebook
   url: https://github.com/BiAPoL/Bio-image_Analysis_with_Python
 
-  authors: Cornelia Wetzker
+- authors: Cornelia Wetzker
   license: cc-by-4.0
   name: Bio-Image Data Strudel for Workshop on Research Data Management in TU Dresden Core Facilities
   description: short introduction to research data management in bio-imaging and NFDI4BIOIMAGING for facilities of TU Dresden Technology Platform
@@ -1235,3 +1235,104 @@ resources:
   - NFDI4BIOIMAGE
   type: slide
   url: https://zenodo.org/records/10083555
+
+- authors: Robert Haase
+  license: cc-by-4.0
+  name: Bio-image Analysis with the Help of Large Language Models
+  description: Large Language Models (LLMs) change the way how we use computers. This also has impact on the bio-image analysis community. We can generate code that analyzes biomedical image data if we ask the right prompts. This talk outlines introduces basic principles, explains prompt engineering and how to apply it to bio-image analysis. We also compare how different LLM vendors perform on code generation tasks and which challenges are ahead for the bio-image analysis community.
+  tags: 
+  - Large Language Models
+  - python
+  type: slide
+  url: https://zenodo.org/records/10815329
+
+- authors: Stephane Rigaud, Brian Northan, Till Korten, Neringa Jurenaite, Apurv Deepak Kulkarni, Peter Steinbach, Sebastian Starke, Johannes Soltwedel, Marvin Albert and Robert Haase
+  license: cc-by-4.0
+  name: PoL Bio-Image Analysis Training School on GPU-Accelerated Image Analysis
+  description: 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
+  type:
+  - notebook
+  url: https://github.com/BiAPoL/PoL-BioImage-Analysis-TS-GPU-Accelerated-Image-Analysis/
+
+- authors: Robert Haase, ScaDS.AI Dresden/Leipzig
+  license: cc-by-4.0
+  name: Bio-image Data Science
+  description: 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
+  type:
+  - notebook
+  url: https://github.com/ScaDS/BIDS-lecture-2024
+
+- authors: Costantin Pape, computational-cell-analytics
+  license: MIT License
+  name: Introduction to Deep Learning for Microscopy
+  description: 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
+  type:
+  - notebook
+  url: https://github.com/computational-cell-analytics/dl-for-micro
+
+- authors: Marcelo Leomil Zoccoler
+  license: cc-by-4.0
+  name: QM Course Lectures on Bio-Image Analysis with napari 2024
+  description: 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
+  type:
+  - notebook
+  url: https://zoccoler.github.io/QM_Course_Bio_Image_Analysis_with_napari_202
+
+- authors: Beth Cimini, Florian Jug, QI 2024
+  license: cc-by-4.0
+  name: QI 2024 Analysis Lab Manual
+  description: This book contains the quantitative analysis labs for the QI CSHL course, 2024
+  tags: 
+  - segmentation
+  - python
+  type:
+  - notebook
+  url: https://bethac07.github.io/qi_2024_analysis_lab_manual/intro.html
+
+- authors: Elnaz Fazeli 
+  license: cc-by-4.0
+  name: My Journey Through Bioimage Analysis Teaching Methods From Classroom to Cloud
+  description: In these slides I introducemy journey through teaching bioimage analysis courses in different formats, from in person courses to online material. I have an overview of different training formats and comparing these for different audiences. 
+  tags: 
+  - teaching
+  type:
+  - slides
+  url: https://zenodo.org/records/10679054
+
+- authors: Robert Haase
+  license: cc-by-4.0
+  name: Cultivating Open Training
+  description: In these slides introduce current challenges and potential solutions for openly sharing training materials, softly focusing on bio-image analysis. In this field a lot of training materials circulate in private channels, but openly shared, reusable materials, according to the FAIR-principles, are still rare. Using the CC-BY license and publicly acessible repositories are proposed to fill this gap.
+  tags: 
+  - teaching
+  type:
+  - slides
+  url: https://zenodo.org/records/10654775
+
+- authors: Josh Moore
+  license: cc-by-4.0
+  name: "[N4BI AHM] Welcome to BioImage Town"
+  description: Keynote at the NFDI4BIOIMAGE All-Hands Meeting in Düsseldorf, Germany, October 16, 2023.
+  tags:
+  - research data management
+  type:
+  - slides
+  url: https://zenodo.org/records/10008465

resources/papers.yml

@@ -91,3 +91,12 @@ resources:
   type:
   - preprint
   url: https://www.biorxiv.org/content/10.1101/2023.10.09.561479v1
+- authors: Dan Chitwood, Sourabh Palande
+  name: Plants & Python - A series of lessons in coding, plant biology, computation, and bioinformatics
+  tags:
+  - notebook
+  type:
+  - publication
+  url:
+  - https://academic.oup.com/plcell/article/34/7/e1/6628764
+  - https://plantsandpython.github.io/PlantsAndPython/00_Opening_page.html

resources/youtube_channels.yml

@@ -17,7 +17,9 @@ resources:
   type:
   - collection
   - video
-  url: https://www.youtube.com/digitalsreeni
+  url:
+  - https://www.youtube.com/digitalsreeni
+  - https://www.youtube.com/watch?v=A4po9z61TME
 - name: Global BioImaging YouTube channel
   type:
   - collection
@@ -111,4 +113,14 @@ resources:
   - Bioimage analysis
   url:
   - https://www.youtube.com/@chrishavlin
-  - https://www.youtube.com/playlist?list=PLqbhAmYZU5KxuAcnNBIxyBkivUEiKswq1
+  - https://www.youtube.com/playlist?list=PLqbhAmYZU5KxuAcnNBIxyBkivUEiKswq1
+- name: RDM4mic
+  license: unknown
+  type:
+  - collection
+  - video
+  tags:
+  - research data management
+  - omero
+  url:
+  - https://www.youtube.com/@RDM4mic