STORM Imaging Analysis

Features: Python, R, MATLAB, Numpy, Scipy, ImageJ/Fiji

Introduction

This project was a collaboration aiming to analyze the nanoclusters of membrane proteins and the interaction between membrane proteins and lipid rafts. The function combined multiple platforms and packages including Python, R (spatstat), MATLAB, and ImageJ/Fiji(Thunderstorm) to employ Ripley's K function, Local-K, density map, and Coordinate-based colocalization.

Instruction

Image: .nd2 files acquired from Nikon d-STORM microscope.

Analytical steps:

1. Script for Fiji imgproc.py:
   1. create folder preprocessing
      • proproimg: split channel and save images individually
      • imgintensity: measure the intensity from a 128*128 central region of image
      • imageinfo
        • imgstat.csv: image information includes following information:
          1. image_name: name of the image
          2. ip_file_name: input file name (with extension)
          3. xSize: frame size on the x-axis
          4. ySize: frame size on the y-axis
          5. nSlices: z dimension
          6. nFrames: t dimension
          7. nChannels: c dimension
          8. size_MB: size of the file in MB
        • imgmetadata: store image metadata for individual files
   2. create folder temp

License

This work is licensed under a Creative Commons Attribution 4.0 International License.