Artificial intelligence (44)#
AI ML DL in Bioimage Analysis - Webinar#
Yannick KREMPP
Published 2024-11-14
Licensed UNKNOWN
A review of the tools, methods and concepts useful for biologists and life scientists as well as bioimage analysts.
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Video, Slides, Webinar
AI4Life teams up with Galaxy Training Network (GTN) to enhance training resources#
Caterina Fuster-Barceló
Licensed UNKNOWN
Tags: Artificial Intelligence, Workflow Engine, Bioimage Analysis
Content type: Documentation
Artificial Intelligence for Digital Pathology#
Jakob Nikolas Kather, Faisal Mahmood, Florian Jug
Published 2024-11-08
Licensed UNKNOWN
How can artificial intelligence be used for digital pathology?
Tags: Artificial Intelligence
Content type: Video
BIDS-lecture-2024#
Robert Haase
Licensed CC-BY-4.0
Training resources for Students at Uni Leipzig who want to dive into bio-image data science with Python. The material developed here between April and July 2024.
Tags: Bioimage Analysis, Artificial Intelligence, Python
Content type: Github Repository
Bio-image Analysis Code Generation using bia-bob#
Robert Haase
Published 2024-10-09
Licensed CC-BY-4.0
In this presentation I introduce bia-bob, an AI-based code generator that integrates into Jupyter Lab and allows for easy generation of Bio-Image Analysis Python code. It highlights how to get started with using large language models and prompt engineering to get high-quality bio-image analysis code.
Tags: Artificial Intelligence, Bioimage Analysis
Bio-image Analysis with the Help of Large Language Models#
Robert Haase
Published 2024-03-13
Licensed CC-BY-4.0
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: Artificial Intelligence, Python
Content type: Slides
Bio-image Data Science#
Robert Haase
Licensed CC-BY-4.0
This repository contains training resources for Students at Uni Leipzig who want to dive into bio-image data science with Python.
Tags: Research Data Management, Artificial Intelligence, Bioimage Analysis, Python
Content type: Notebook
Bio-image Data Science Lectures @ Uni Leipzig / ScaDS.AI#
Robert Haase
Licensed CC-BY-4.0
These are the PPTx training resources for Students at Uni Leipzig who want to dive into bio-image data science with Python. The material developed here between April and July 2024.
Tags: Bioimage Analysis, Artificial Intelligence, Python
Content type: Slides
BioEngine#
Jeremy Metz, Beatriz Serrano-Solano, Wei Ouyang
Licensed UNKNOWN
BioEngine is a cloud infrastructure to run BioImage model zoo based workflows in the cloud.
Tags: Artificial Intelligence, Workflow Engine
Content type: Publication
BioEngine Documentation#
Wei Ouyang, Nanguage, Jeremy Metz, Craig Russell
Licensed MIT
BioEngine, a Python package designed for flexible deployment and execution of bioimage analysis models and workflows using AI, accessible via HTTP API and RPC.
Tags: Workflow Engine, Artificial Intelligence, Python
Content type: Documentation
BioImage Archive AI Gallery#
Licensed CC0-1.0
Tags: Bioimage Analysis, Artificial Intelligence
Content type: Collection, Data
Bioimage Model Zoo#
Licensed UNKNOWN
Tags: Bioimage Analysis, Artificial Intelligence
Content type: Collection
Building a Bioimage Analysis Workflow using Deep Learning#
Estibaliz Gómez-de-Mariscal
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Slides
CARE/Stardist tutorials for EMBO Practical Course — Computational optical biology 2022#
Martin Weigert
Licensed UNKNOWN
Tags: Python, Artificial Intelligence, Bioimage Analysis
Content type: Notebook
CSBDeep and StarDist @ I2K 2020#
Martin Weigert, Uwe Schmidt
Licensed UNKNOWN
Tags: Python, Artificial Intelligence, Bioimage Analysis
Content type: Notebook
Collection of teaching material for deep learning for (biomedical) image analysis#
Constantin Pape
Licensed MIT
Tags: Artificial Intelligence, Bioimage Analysis
Course on Deep Learning for imaging using PyTorch#
Guillaume Witz
Licensed UNKNOWN
Tags: Python, Bioimage Analysis, Artificial Intelligence
Content type: Notebook
Creating a Research Data Management Plan using chatGPT#
Robert Haase
Published 2023-11-06
Licensed CC-BY-4.0
In this blog post the author demonstrates how chatGPT can be used to combine a fictive project description with a DMP specification to produce a project-specific DMP.
Tags: Research Data Management, Artificial Intelligence
Content type: Blog Post
https://focalplane.biologists.com/2023/11/06/creating-a-research-data-management-plan-using-chatgpt/
DEEP NAPARI : Napari as a tool for deep learning project management#
Herearii Metuarea, David Rousseau, Pejman Rasti, Valentin Gilet
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Notebook
DL@MBL 2021 Exercises#
Jan Funke, Constantin Pape, Morgan Schwartz, Xiaoyan
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Slides, Notebook
Deep Learning Based Segmentation For Biologists#
Licensed AGPL-3.0
Tags: Python, R, Artificial Intelligence
Content type: Notebook
Deep Learning for image analysis - Exercises#
Martin Weigert
Licensed UNKNOWN
Tags: Fiji, Artificial Intelligence, Bioimage Analysis
Content type: Notebook
Deep Vision and Graphics#
Victor Yurchenko, Fedor Ratnikov, Viktoriia Checkalina
Licensed MIT
Tags: Python, Artificial Intelligence
Content type: Notebook
DeepProfiler Handbook#
Michael Bornholdt, Juan Caicedo, Yu Han, Nikita Moshkov, Rebecca Senft
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Book
cytomining/DeepProfiler-handbook
https://cytomining.github.io/DeepProfiler-handbook/docs/00-welcome.html
Dr Guillaume Jacquemet on studying cancer cell metastasis in the era of deep learning for microscopy#
Guillaume Jacquemet
Published 2024-10-24
Licensed UNKNOWN
Leukocyte extravasation is a critical component of the innate immune response, while circulating tumour cell extravasation is a crucial step in metastasis formation. Despite their importance, these extravasation mechanisms remain incompletely understood. In this talk, Guillaume Jacquemet presents a novel imaging framework that integrates microfluidics with high-speed, label-free imaging to study the arrest of pancreatic cancer cells (PDAC) on human endothelial layers under physiological flow conditions.
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Video, Slides
EMBL Deep Learning course 2019 exercises and materials#
Valentyna Zinchenko, Pejman Rasti, Martin Weigert, Szymon Stoma
Licensed UNKNOWN
Tags: Python, Artificial Intelligence
Content type: Notebook
EMBL Deep Learning course 2021/22 exercises and materials#
Martin Weigert, Constantin Pape
Licensed UNKNOWN
Tags: Python, Artificial Intelligence
Content type: Notebook
EMBL Deep Learning course 2023 exercises and materials#
Martin Weigert, Uwe Schmidt, Benjamin Gallusser, Albert Dominguez Mantes, Buglakova Alyona
Licensed UNKNOWN
Tags: Python, Artificial Intelligence
Content type: Notebook
FAIRy deep-learning for bioImage analysis#
Estibaliz Gómez de Mariscal
Licensed CC-BY-4.0
Introduction to FAIR deep learning. Furthermore, tools to deploy trained DL models (deepImageJ), easily train and evaluate them (ZeroCostDL4Mic and DeepBacs) ensure reproducibility (DL4MicEverywhere), and share this technology in an open-source and reproducible manner (BioImage Model Zoo) are introduced.
Tags: Artificial Intelligence, FAIR-Principles, Bioimage Analysis
Content type: Slides
Generative artificial intelligence for bio-image analysis#
Robert Haase
Licensed CC-BY-4.0
Tags: Python, Bioimage Analysis, Artificial Intelligence
Content type: Slides
Introduction to Deep Learning for Microscopy#
Costantin Pape
Licensed MIT
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: Artificial Intelligence, Python
Content type: Notebook
Kreshuk Lab’s EMBL EIPP predoc course teaching material#
Adrian Wolny, Johannes Hugger, Qin Yu, Buglakova Alyona
Licensed UNKNOWN
Tags: Artificial Intelligence
Content type: Tutorial
Large Language Models: An Introduction for Life Scientists#
Robert Haase
Published 2024-12-12
Licensed CC-BY-4.0
This slide deck introduces Large Language Models to an audience of life-scientists. We first dive into terminology: Different kinds of Language Models and what they can be used for. The remaining slides are optional slides to allow us to dive deeper into topics such as tools for using LLMs in Science, Quality Assurance, Techniques such as Retrieval Augmented Generation and Prompt Engineering.
Tags: Globias, Artificial Intelligence
Machine Learning - Deep Learning. Applications to Bioimage Analysis#
Estibaliz Gómez-de-Mariscal
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Slides
Machine and Deep Learning on the cloud: Segmentation#
Ignacio Arganda-Carreras
Licensed UNKNOWN
Tags: Neubias, Artificial Intelligence, Bioimage Analysis
Content type: Slides
MicroSam-Talks#
Constantin Pape
Published 2024-05-23
Licensed CC-BY-4.0
Talks about Segment Anything for Microscopy: computational-cell-analytics/micro-sam. Currently contains slides for two talks:
Overview of Segment Anythign for Microscopy given at the SWISSBIAS online meeting in April 2024 Talk about vision foundation models and Segment Anything for Microscopy given at Human Technopole as part of the EMBO Deep Learning Course in May 2024
Tags: Bioimage Analysis, Artificial Intelligence
Content type: Slides
Microscopy data analysis: machine learning and the BioImage Archive#
Andrii Iudin, Anna Foix-Romero, Anna Kreshuk, Awais Athar, Beth Cimini, Dominik Kutra, Estibalis Gomez de Mariscal, Frances Wong, Guillaume Jacquemet, Kedar Narayan, Martin Weigert, Nodar Gogoberidze, Osman Salih, Petr Walczysko, Ryan Conrad, Simone Weyend, Sriram Sundar Somasundharam, Suganya Sivagurunathan, Ugis Sarkans
Licensed CC-BY-4.0
The Microscopy data analysis: machine learning and the BioImage Archive course, which focused on introducing programmatic approaches used in the analysis of bioimage data via the BioImage Archive, ran in May 2023.
Tags: Bioimage Analysis, Python, Artificial Intelligence
Content type: Video, Slides
Neubias Academy 2020: Introduction to Nuclei Segmentation with StarDist#
Martin Weigert, Olivier Burri, Siân Culley, Uwe Schmidt
Licensed UNKNOWN
Tags: Python, Neubias, Artificial Intelligence, Bioimage Analysis
Content type: Slides, Notebook
NeubiasPasteur2023_AdvancedCellPose#
Gaelle Letort
Licensed BSD-3-CLAUSE
Tutorial for running CellPose advanced functions
Tags: Bioimage Analysis, Artificial Intelligence
Content type: Github Repository
Running Deep-Learning Scripts in the BiA-PoL Omero Server#
Marcelo Zoccoler
Licensed CC-BY-4.0
Tags: Python, Artificial Intelligence, Bioimage Analysis
Content type: Blog Post
https://biapol.github.io/blog/marcelo_zoccoler/omero_scripts/readme.html
Training Deep Learning Models for Vision - Compact Course#
Constantin Pape, Adrian Wolny
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
ZIDAS 2020 Introduction to Deep Learning#
Estibaliz Gómez-de-Mariscal
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Slides
ilastik: interactive machine learning for (bio)image analysis#
Anna Kreshuk, Dominik Kutra
Licensed CC-BY-4.0
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Slides
introduction-to-generative-ai#
Bruna Piereck, Alexander Botzki
Published 2024-09-27T14:38:51+00:00
Licensed CC-BY-4.0
Course repository for Strategic Use of Generative AI
Tags: Artificial Intelligence
Content type: Github Repository, Tutorial
vibbits/introduction-to-generative-ai