Code repository for Pix2D diffusivity mapping.
Requires matlab-storm published by Zhuanglab (https://github.com/ZhuangLab/matlab-storm)
Codes are written to process images in .dax format and localization data from Insight3.
Localization with Insight3 can be replaced with Python: https://github.com/ZhuangLab/storm-analysis
- Use codes under Matlab > Simulation
- Training sets with multiple single-molecule brightness and shot noise level can be generated with Batch_Training_set_generation.m
- Set exposure time, pixel length, gain factor and PSF size to match your imaging setup.
- Run localization analysis to generated Dax image files.
- Generate training input from .dax and .bin file with Training_set_extraction.m
- Generate augmented training input with training_set_combine.m
- Use codes under Matlab > Training
- To sweep hyperparamters, run Batch_training_parameter_sweep.m
- Run Batch_training.m for to get trained CNN
- Run localization for single-molecule images
- Use Data sampling > Batch_ROI_extraction to extract single-molecule signals and positions
- Run Data processing > Batch_D_mapper_from_array.m to generate spatial diffusivity map in desired bin size
- Run Data processing > Dmap_rendering.m to plot 2D diffusivity map in color scale
Contact: Ha Park (ha.park@berkeley.edu)