Welcome to pie’s documentation!

Processing Images Easily (PIE) automatically tracks growing microcolonies in low-resolution brightfield and phase-contrast microscopy images. The program works for recognizing microcolonies in a wide range of microbes, and allows automated measurement of growth rate, lag times, and (if applicable) fluorescence across time for microcolonies founded by single cells. PIE recognizes colony outlines very robustly and accurately across a wide range of image brightnesses and focal depths, and allows simultaneous measurements of growth properties and fluorescence intensities with very high throughput (in our lab, ~100,000 colonies per experiment), including in complex, multiphase experiments.

See the PIE preprint for details on the analysis, and the PIE github repository for the code.

To test microcolony recognition and growth tracking on your images, try our web application.

If you have any questions about setting up or using PIE, we’d love to help! Feel free to contact us at pie-siegal-lab@nyu.edu or open an issue on github.

• PIE Quickstart

Install upgrade and uninstall

• Install and upgrade PIE
• Uninstall PIE

Inputs and outputs

• PIE Inputs
• PIE Outputs

Running PIE

• Running PIE single-image analysis
• Running PIE timelapse experiments
• Parallelizing PIE analysis

Making Movies

• Creating movies of image analysis results
  • Creating default microcolony growth movies
  • Creating movies with custom microscopy views, plots, and frame arrangements
  • Creating cell movies
  • Saving movies
  • Creating and blending fluorescence movies
  • Creating post-phase fluorescence movies
  • Creating plots
  • Combining movie panels

Sample Experimental Data

• Sample Experiments
  • Downloading example experiments
  • Example data

Indices and tables

• Index

• Module Index

• Search Page