epitope_barcoding

Code and sample data generated for "A multiplexed epitope barcoding strategy that enables dynamic cellular phenotypic screens".

Sequence analysis for linking NNNs and epitopes

python src/seq_analysis.py

This produces nandbar.npz which contains a list of a pair of NNN sequences and the associated epitope combinations.

Aligning and unmixing

python tests/tests_align.py
python tests/tests_unmixing.py

Live-cell analysis

data also contains sample setting files of CellTK for tracking live single-cell trajectories.

data/livecell_celltk0.yml
data/livecell_celltk1.yml

For U-Net based segmentation, it requires pre-trained weights in HDF5 file. The hdf5 file is produced by training dataset with CellUNet.