amgfernandes/FIJI_Clij2_GPU_Weka_ML_course

Jupyter NotebookNOASSERTION

FIJI Clij2 GPU Weka ML course

Introduction to Bioimage analysis for Master of Science (M.Sc.) in Neurosciences

In preparation for the course please install in advance:

FIJI: https://imagej.net/software/fiji/

Python/Anaconda installation (optional): https://docs.anaconda.com/anaconda/install/

Download or use Git to clone this repository:

You can use Download ZIP or Git: git clone https://github.com/amgfernandes/FIJI_Clij2_GPU_Weka_ML_course.git

For the python part:

You can create a new environment called bioimage:

cd python_visualization

conda create --name bioimage -y

conda activate bioimage

conda install pip -y

pip install -r requirements.txt

And add your new env kernel to your jupyter

conda install -c anaconda ipykernel

python -m ipykernel install --user --name=bioimage

Bioimage Analysis: Recommended Reading and Viewing:

Python: Basics for Data Scientists --> https://github.com/FabrizioMusacchio/Python_Course
Introduction to Bioimage Analysis --> https://bioimagebook.github.io/README.html
Introduction to Bioimage Analysis video --> https://www.ibiology.org/techniques/introduction-to-bioimage-analysis/
Bioimage analysis for computational biology --> https://github.com/BiAPoL/Bio-image_Analysis_with_Python
Introduction to Image Analysis with FIJI --> https://www.crick.ac.uk/sites/default/files/2018-07/Introduction%20to%20image%20analysis%20with%20FIJI_David%20Berry_TheFrancisCrickInstitute_0.pdf
ML for Bioimage analysis --> https://montpellierressourcesimagerie.github.io/mri-workshop-machine-learning/slides_day1.revealjs.htm#/3
Napari (Multi-dimensional image viewer for python): https://napari.org/stable/