myimg 0.4

Batch processing of micrographs

MyImg :: Processing of micrographs

• MyImg is a toolbox for the processing of micrographs, which can:
  1. Process single micrographs (improve contrast, insert scalebars, etc.).
  2. Prepare high-quality tiled images from the processed micrographs.
  3. Run additional applications such as:
     • FFT = 2D Fourier transforms
     • MDistr = size distributions from series of micrographs
     • iLabels = find and categorize nanoparticles on (S)TEM micrographs

Principle

• TODO

Installation

• Requirement: Python with sci-modules: numpy, matplotlib, pandas
• pip install scikit-image = additional package for image processing
• pip install myimg = MyImg package itself (uses all packages above)

Quick start

• Jupyter notebooks with comments:
  • Example 1 :: MyImage :: process single image(s)
  • Example 2 :: MyReport :: create nice, publication-ready image reports
  • Example 3 :: Apps/FFT :: calculate and analyze 2D Fourier transforms
• Complete set of examples including testing data at DropBox.

Documentation, help and examples

• PyPI repository.
• GitHub repository.
• GitHub Pages with help and complete package documentation.

Versions of MyImg

• Version 0.1 = 1st draft: too complex, later completely re-written
• Version 0.2 = 2nd draft: MyImage object with cut, crop, label, scalebar
• Version 0.3 = objects: MyImage, MyReport; apps: FFT, iLabels (semi-finished)
• Version 0.4 = apps.velox: utilities to process Velox EMD files
• Version 0.5 = TODO: add scalebar-stripes, mdistr + finalize FFT, iLabels