SuperResNET Batch

This repo holds the SuperResNET batch pipeline using V3.0 of SuperResNET designed by Ismail Khater.

Also contains work written by Christian Hallgrimson, Ben Cardoen, & Mona Shahsavari.

For GUI SuperResNET please see: medicalimageanalysis.com/software/superresnet

Citation

If you make use of this work, please cite:

@Article{KhaterSR2018,
title={Super Resolution Network Analysis Defines the Molecular Architecture of Caveolae and Caveolin-1 Scaffolds},
author={Khater, Ismail M. and Meng, Fanrui and Wong, Timothy H. and Nabi, Ivan Robert and Hamarneh, Ghassan},
journal={Scientific Reports},
year={2018},
url={https://doi.org/10.1038/s41598-018-27216-4}
}

Usage

The pipeline can be run directly on a single file from the commmand line:

matlab -nodesktop -nosplash -r "pipeline <input_dir/> <file_name/> <output_dir/> \
min_X max_X min_Y max_Y min_Z max_Z \
merge_threshold alpha_noise proximity_threshold kernal_bandwidth \
Xconv Yconv Zconv; quit" 

or within matlab:

pipeline(input_dir, file_name, output_dir, min_X, max_X, min_Y, max_Y, min_Z, max_Z, merge_threshold, alpha_noise, proximity_threshold, kernal_bandwidth, Xconv, Yconv, Zconv);

The file "slurm_submit.sh" provides an easy-to-use script for submitting to a cluster using SLURM, jobs will be submitted across multiple cores (A job per input file). Usage instructions and parameters required are explained within the file. It is recommended to create a copy of this file for every experiment. To submit the script you can use the command:

sbatch --array=1-$(./easy_submit.sh -a) easy_submit.sh

Parameters

input_dir: Directory containing the data to process
file_name: File to process. Supports the extensions, .ascii, .bin. txt, .csv, .d3dlp
output_dir: Where to save the results. (Note that the output filename is based on the input filename). Set to "same" to place results in the same location as the input file.
min_X, max_X, min_Y, max_Y, min_Z, max_Z: Region of interest
merge_threshold, alpha_noise, proximity_threshold, kernal_bandwidth: SuperResNET Parameters
Xconv, Yconv, Zconv: Unit conversions to nm. The value should be such that, "Localizations provided" * conv = "Localizations in nm"

Grouping

The SuperResNET grouping functionality is given in the "Grouping/" folder. Fill in the script "Grouping/group.m" as described in the file. It is recommended to create a copy for each experiment. The script can run directly in the command line with:

matlab -nodesktop -nosplash -r "run(group.m); quit"

or within matlab by using the run button with the script open or by using the command:

run(group.m)

Requirements

• Matlab
• Clone of this repo. All dependencies are included.