Tutorial

The below assumes you have the source code installed as per the installation instructions.

The Parameter selection and tuning. section will explain what parameters there are, and guide you through the parameter selection.

Processing a single cell (3D STED) with two channels

julia --project=. scripts/ercontacts.jl -i <data> -o <output>

Processing a dataset with multiple channels

julia --project=. scripts/batch.jl -i <data> -o <output> -r "*[1,2,3].tif"

This expects the data to be organized like so

- top folder
  - replicate number
    - cell type
      - Seriesxyz 
        - ...0.tif
        - ...1.tif
        - ...2.tif 
        - ...3.tif
        - ...4.tif

In this case the "*[1,2,3].tif" parameters indicate that you want contacts between the pairs of channels of files ending with 1,2, and 3. The code will check your data, and if those files are there, you will get output like

1--2/
    replicate 
        cell 
            ...
1--3/
2--3/

See PostProcessing on instruction on how to curate, aggregate and postprocess the outcome.

Interactive usage

In VSCode, navigate to demo.jl

If you have Julia and its plugin installed, you can now evaluate code line by line.

For example:

This would work like this:

using Pkg; Pkg.activate("."); # <CTRL+ENTER>
using SubPrecisionContactDetection; # <CTRL+ENTER>
@info "Test"; #CTRL+ENTER
defs = get_defaults(); #CTRL+ENTER

Julia API

While you can call the scripts from the command line, you can also do so from within Julia:

using SubPrecisionInteractionDetection
twochannel_contats(get_defaults());