# SiteLocalization
Binding site localization on non-homogeneous cell surfaces using topological image averaging

## Usage
![Usage Example](../assets/tty.gif?raw=true)

```
usage: run.jl [--pixelsize PIXELSIZE] [--shiftwindow SHIFTWINDOW]
              [--iterations ITERATIONS] [--margin MARGIN]
              [--votingthreshold VOTINGTHRESHOLD] [--rmin RMIN]
              [--rmax RMAX] [--pxmult PXMULT]
              [--snr-ratio-limit SNR-RATIO-LIMIT] [--limit-outside]
              [--maxdist MAXDIST] [--debug-plots] [-h] images...

positional arguments:
  images                images to analyze

optional arguments:
  --pixelsize PIXELSIZE
                        image pixel size in nanometers (type: Float64,
                        default: 20.5333)
  --shiftwindow SHIFTWINDOW
                        sliding average window (type: Int64, default:
                        7)
  --iterations ITERATIONS
                        RL iterations (type: Int64, default: 0)
  --margin MARGIN       fitted circle radius margin (type: Int64,
                        default: 20)
  --votingthreshold VOTINGTHRESHOLD
                        sensitivity of circle detection in pixels
                        (type: Int64, default: 20)
  --rmin RMIN           fitted circle minimum radius (type: Int64,
                        default: 36)
  --rmax RMAX           fitted circle maximum radius (type: Int64,
                        default: 44)
  --pxmult PXMULT       pixel interpolation (type: Float64, default:
                        2.0)
  --snr-ratio-limit SNR-RATIO-LIMIT
                        SNR limit in terms of ratio to SNR of first
                        frame at which to stop analyzing a time
                        sequence (type: Float64, default: 0.3)
  --limit-outside       limit search for peaks to outside of reference
                        channel
  --maxdist MAXDIST     maximum distance from reference channel within
                        which to search for peaks (type: Int64,
                        default: 0)
  --debug-plots         enable saving of plots and images for
                        debugging purposes
  -h, --help            show this help message and exit
```

## Abstract
Antibody binding to cell surface proteins plays a crucial role
in immunity and the location of an epitope can altogether determine
the immunological outcome of a host-target interaction.
Techniques available today for epitope identification are
costly, time-consuming, and unsuited for high-throughput analysis.
Fast and efficient screening of epitope location can be
useful for the development of therapeutic monoclonal antibodies and vaccines.
In the present work, we have developed a method for imaging-based localization
of binding sites on cellular surface proteins.
The cellular morphology typically varies,
and antibodies often bind in a non-homogenous manner, making
traditional particle-averaging strategies challenging for accurate
native antibody localization. Nanometer-scale resolution
is achieved through localization in one dimension, namely the
distance from a bound ligand to a reference surface, by using
topological image averaging. Our results show that this method
is well suited for antibody binding site measurements on native
cell surface morphology.