SL2PM

A package for tracking particles, red blood cells (RBCs), and microvessel walls with super-localization from images recorded with two-photon microscopy (2PM).

To get started with SL2PM, explore tutorials for tracking quantum dots, red blood cells, and capillaries. For example, if you are interested in measuring diameter of a capillary, made visible with fluorescently-labeled plasma (e.g. with FITC-dextran), see Tracking a capillary demo.

All tracking algorithms require calibration of the microscope’s photomultiplier tubes (Calibrating photomultiplier tubes) and, for tracking capillaries, calibration of the microscope’s point-spread function (Calibrating point-spread function for microvessel tracking).

The data analysis in SL2PM is data-driven, i.e., you need to check if underlying assumptions of SL2PM analysis are satisfied in your data before you apply any function from SL2PM. This is why we suggest using SL2PM with Jupyter notebooks, where you can explore your data step-by-step (following our examples) and tailor SL2PM analysis to your data, if needed.

Contents:

• sl2pm
  • sl2pm package

Tracking a quantum dot

• Demo for how to track single quantum dots on images
  • Tracking a single quantum dot, visualising and inspecting the fits

Tracking a red blood cell

• Demo for how to track a single RBC from its kymogram and estimate the RBC’s speed
  • Tracking a single RBC, visualising and inspecting the fits
  • Estimating the RBC’s speed

Tracking a capillary

• Demo for how to track a capillary (estimate radius and center position) with fluorescently-labeled plasma
  • Calibrating the microscope’s PSF
  • Preparing fluorescence line-profiles for fitting
  • Tracking the capillary’s center and radius by fitting line-profiles of fluorescence
  • Visualizing the tracking results
  • Inspecting the fits

Calibrating photomultiplier tubes

• Demo for how to quickly calibrate photomultiplier tubes (PMT) on your two-photon microscope (2PM)

Calibrating point-spread function for microvessel tracking

• Demo for how to calibrate PSF for estimating vessels diameters with super-localization
  • Protocol A (both plasma and wall fluorescence)
  • Protocol B (only plasma fluorescence)
  • Protocol C (only wall fluorescence)

Calibrating point-spread function for microvessel tracking with the `ultimate fit`

• Demo for how to track a blood vessel in time and calibrate the microscope’s PSF in a single fit (“ultimate fit”).
  • Protocol A: The Ultimate Fit (both plasma and wall fluorescence)
  • Protocol B: The Ultimate Fit (only plasma fluorescence)
  • Protocol C: The Ultimate Fit (only wall fluorescence)

Removing artefact from output of photomultiplier tubes

• Demo for how to fit a single period of biastable bias for further removal

Indices and tables

• Index

• Module Index

• Search Page