Developed within the Weinstein Lab at the University of Chicago.

DNA microscopy is a new technology development program to achieve spatio-genetic imaging without the use of specialized machinery.

• Use pyenv or virtualenv to establish python=2.7.15+. (I know, we'll be upgrading this to Python 3 ASAP).
• Use pip to install requirements, e.g. python2 -m pip install -r requirements.txt.

Save a 3D file of positions to ./posfile.csv with the following columns (no header row):

1. Point index
2. Boolean index, 0 for beacon and 1 for target. (Recommend randomly dividing half your points into beacons and targets)
3. X position
4. Y position
5. Z position

Execute script ./run_dnamic.sh, which will copy the position file to the proper directory, run simulation/inference code (can take up to 20-30 minutes depending on your hardware), and copy the final inferred positions back to the root directory.