Analyze nuclear translocation of proteins in 3D confocal imaging

Checking nuclear translocation of proteins using Voronoi-Otsu labeling and label erosion from pyclesperanto

Instructions

In order to run these Jupyter notebooks and .py scripts you will need to familiarize yourself with the use of Python virtual environments using Mamba. See instructions here.
Then you will need to create a virtual environment using the following command:

mamba create -n nuclear_translocation python=3.9 devbio-napari boto3 plotly pyqt -c conda-forge
Run the 0_data_download.ipynb notebook to fetch the raw_data from an AWS S3 bucket. Contact Me to obtain a fresh working link.
The next 3 notebooks allow you to analyze all images, explore the results and visualize in detail the segmentation using Napari.

Name		Name	Last commit message	Last commit date
Latest commit History 15 Commits
images		images
.gitignore		.gitignore
00_presigned_url_generator.ipynb		00_presigned_url_generator.ipynb
0_data_download.ipynb		0_data_download.ipynb
1_image_analysis.ipynb		1_image_analysis.ipynb
2_data_exploration.ipynb		2_data_exploration.ipynb
3_visualization.ipynb		3_visualization.ipynb
LICENSE		LICENSE
README.md		README.md
utils.py		utils.py