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
orvirtualenv
to establishpython=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):
- Point index
- Boolean index, 0 for beacon and 1 for target. (Recommend randomly dividing half your points into beacons and targets)
- X position
- Y position
- 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.