Input data:
- 3D video (.tif)
- Particle tracking file (.csv). The tracking file minimally requires columns (in any order):
'TRACK_ID', 'POSITION_T', 'POSITION_Y', and 'POSITION_X'
Output data: files produced from SMT python code
To run the jupyter notebook, make sure you have the following programs installed on your computer.
https://www.python.org/downloads/mac-osx/
Make sure you have python3 installed:
python --version
bash ~/Downloads/Anaconda3-2020.02-MacOSX-x86_64.sh
https://www.anaconda.com/products/individual
If you already have anaconda updated, make sure you have the latest version:
conda update --all
pip install --upgrade pip
pip install napari[all]
pip install PyQt5
pip install -U scikit-learn
https://www.anaconda.com/products/individual
go to "environments"
add "conda-forge" into channels
select "Not installed"
type "Napari" in the search field
add Napari
Napari should run without installing PyQt5 (I think), but it will give a warning message about qt library version
you can remove this warning message by installing PyQt5 from Terminal (updating qt from Anaconda-Navigator did not work for me)
pip install PyQt5
Do not try to update all libraries from terminal (conda update --all). I got many problems after updating all libraries.
In a command terminal, open jupyter notebook:
jupyter notebook
When redirected to a the online interface, upload the python code:
- Download tracking code from this GitHub repository
- Upload it into the jupyter notebook web gui
- optional: Download additional input data files from this GitHub repository if you wish to use them to test the code