This page was created by the AI4Life project using data provided by Katharina Hennig at Institute of Molecular Medicine (now Gulbenkian Institute for Molecular Medicine). All the images demonstrated in this tutorial are provided under CC-BY licence.
If any of the instructions are not working, please open an issue or contact us at ai4life@fht.org!
Project challenges: cell instance segmentation.
A 3D human motor neuron disease platform for high throughput drug screening. The goal of this package is to load the 3D images acquired of neurospheres and segment nuclei and Islet1 positive nuclei from their respective channels.
The dataset used for this project can be found in BioImage Archive with accession number S-BIAD1737.
Install the conda package, dependency and environment manager.
You can download this repository from the green Code button and download and zip, or through the command line with
cd <path to any folder of choice>
git clone https://github.com/BIIFSweden/AI4Life_OC2_2024_38.git
Then create the neuroscan conda environment:
cd <path to your 'AI4Life_OC2_2024_38' directory>
conda env create -f environment.yml
This will install all necessary project dependencies as well as the neuroscan companion package (editable install).
Copy all project data to the data directory (or use symbolic links).
Then run Jupyter Lab from within the neuroscan conda environment:
cd <path to your 'AI4Life_OC2_2024_38' directory>
conda activate neuroscan
jupyter-lab
All analysis notebooks can be found in the notebooks directory.
Or you can use the following command to analyze a folder.
conda activate neuroscan
neuroscan segment <path to folder>
This will add two TIFF labeled images containing the instance segmentation for nuclei and motor neurons in separate files.
Should you want to delve deeper into how the pipeline was developed, please go to the notebooks folder.
You can find three notebooks.
The data_loading.ipynb describes how images are loaded.
The nuclei_segmentation.ipynb describes how nuclei are segmented from the nuclei channel.
The motor_segmentation.ipynb describes how motor neurons are segmented from the motor neuron channel.
AI4Life is a Horizon Europe-funded project that brings together the computational and life science communities.
AI4Life has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement number 101057970. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.
If you find a bug, please raise an issue.
Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.
SciLifeLab BioImage Informatics Facility (BIIF) project lead: Agustin Corbat
Data acquisition: Katharina Hennig, Afonso Malheiro, Edgar R. Gomes