FrickTobias / nd2tools

ND2 image handling package

A package for automating the most common ND2 exports, like to PNG images or MP4 timelapse videos. This is an ongoing development process where features are continuously added.

Feel free to post suggestions of what functionality to add by opening an issue.

Requirements

Install miniconda according to their instructions or use the script in this git repo.

bash install-miniconda.sh

Installing

Run this in your terminal.

git clone https://github.com/FrickTobias/nd2tools.git 
conda env create -n ndt -f nd2tools/environment.yml 
conda activate ndt
pip install -e nd2tools 

Updating

git -C path/to/nd2tools pull

Usage

See nd2tools -h and nd2tools [display|image|movie] -h .

Minimal examples

View image

nd2tools display cells.nd2 

Write image

nd2tools image cells.nd2 cells.png

Make movie

nd2tools movie cells.nd2 cells.mp4

Option usage examples

Split into a 2x2 grid and write to separate PNGs

nd2tools image cells.nd2 cells.png --split 2 2 --keep 0 0

Add scalebar and timestamps and write movie

nd2tools movie cells.nd2 cells.mp4 --scalebar --timestamps