Mit (24)#
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, Deep Learning, Python
Content type: Documentation
CellTrackColab#
Guillaume Jacquemet
Licensed MIT
Content type: Notebook, Collection
Collection of teaching material for deep learning for (biomedical) image analysis#
Constantin Pape
Licensed MIT
Tags: Artificial Intelligence, Bioimage Analysis
Data Carpentry for Biologists#
Licensed [‘CC-BY-4.0’, ‘MIT’]
Content type: Tutorial, Code
Deep Vision and Graphics#
Victor Yurchenko, Fedor Ratnikov, Viktoriia Checkalina
Licensed MIT
Tags: Python, Artificial Intelligence
Content type: Notebook
FriendsDontLetFriends#
C. Li
Published 2024-03-10T15:34:07+00:00
Licensed MIT
Friends don’t let friends make certain types of data visualization - What are they and why are they bad.
Tags: Visualization
Content type: Github Repository
Galaxy Training Material#
Licensed MIT
Content type: Slides, Tutorial
Image analysis course material#
Christian Tischer
Licensed MIT
Training materials about image registration, big warp and elastix
Image processing with Python#
Guillaume Witz
Licensed MIT
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.
Tags: Python
Content type: Notebook
Intro napari slides#
Peter Sobolewski
Licensed MIT
Introduction to napari workshop run at JAX (Spring 2024).
Tags: Napari
Content type: Slides
https://thejacksonlaboratory.github.io/intro-napari-slides/#/section
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: Deep Learning, Pytorch, Segmentation, Python
Content type: Notebook
LauLauThom/MaskFromRois-Fiji: Masks from ROIs plugins for Fiji - initial release#
Laurent Thomas, Pierre Trehin
Published 2021-07-22
Licensed MIT
Fiji plugins for the creation of binary and semantic masks from ROIs in the RoiManager. Works with stacks too.
Installation in Fiji: activate the Rois from masks update site in Fiji.
See GitHub readme for the documentation.
Latest tested with Fiji 2.1.0/ImageJ 1.53j
NLP Course#
Yandex School of Data Analysis
Licensed MIT
YSDA course in Natural Language Processing
Tags: Natural Language Processing
Content type: Github Repository
OMERO - HCS analysis pipeline using Jupyter Notebooks#
Riccardo Massei
Licensed MIT
Material and solutions for the course ‘Bioimage data management and analysis with OMERO’ held in Heidelberg (13th May 2024) - Module 3 (1.45 pm - 3.45 pm): OMERO and Jupyter Notebooks. Main goal of the workflow is to show the potential of JN to perform reproducible image analysis in connection with an OMERO instance. In this specific example, we are performing a simple nuclei segmentation from raw images uploaded in OMERO.
Tags: Teaching, Bioimage Analysis, Notebooks, Python, OMERO
Content type: Github Repository
Prompt-Engineering-LLMs-Course#
Published 2024-09-11T07:45:30+00:00
Licensed MIT
Tags: Llms, Prompt Engineering, Code Generation
Content type: Github Repository, Tutorial
HelmholtzAI-Consultants-Munich/Prompt-Engineering-LLMs-Course
Python BioImage Analysis Tutorial#
Jonas Hartmann
Licensed MIT
Tags: Python, Bioimage Analysis
Python for Microscopists#
Sreenivas Bhattiprolu
Licensed MIT
Tags: Python, Bioimage Analysis
Content type: Notebook, Collection
Teaching Bioimage Analysis with Python#
Rafael Camacho
Licensed MIT
Tags: Python, Bioimage Analysis
Content type: Tutorial
Teaching ImageJ FIJI#
Rafael Camacho
Licensed MIT
Tags: Fiji, Bioimage Analysis
Content type: Tutorial
The Turing Way: Guide for reproducible research#
Licensed [‘CC-BY-4.0’, ‘MIT’]
A guide which covers topics related to skills, tools and best practices for research reproducibility.
Content type: Book
https://the-turing-way.netlify.app/reproducible-research/reproducible-research
Workshop-June2024-Madrid#
Licensed MIT
Tags: Bioimage Analysis
Content type: Workshop, Collection
YMIA - Python-Based Event Series Training Material#
Riccardo Massei, Robert Haase, ENicolay
Published None
Licensed MIT
This repository offer access to teaching material and useful resources for the YMIA - Python-Based Event Series.
Tags: Python, Large Language Models, Prompt Engineering, Biabob, Bioimage Analysis, Microscopy Image Analysis
Content type: Github Repository, Slides
ZeroCostDL4Mic: exploiting Google Colab to develop a free and open-source toolbox for Deep-Learning in microscopy#
Lucas von Chamier, Romain F. Laine, Johanna Jukkala, Christoph Spahn, Daniel Krentzel, Elias Nehme, Martina Lerche, Sara Hernández-pérez, Pieta Mattila, Eleni Karinou, Séamus Holden, Ahmet Can Solak, Alexander Krull, Tim-Oliver Buchholz, Martin L Jones, Loic Alain Royer, Christophe Leterrier, Yoav Shechtman, Florian Jug, Mike Heilemann, Guillaume Jacquemet, Ricardo Henriques
Licensed MIT
Content type: Notebook, Collection
cba-support-template#
Arif Khan, Christian Tischer, Sebastian Gonzalez, Dominik Kutra, Felix Schneider, et al.
Published 2021-12-01
Licensed MIT
Tags: Workflow, Research Data Management
Content type: Tutorial
https://git.embl.de/grp-cba/cba-support-template