The PYthon Microscopy Environment

The PYthon Microscopy Environment is an open-source package providing image acquisition and data analysis functionality for a number of microscopy applications, but with a particular emphasis on single molecule localisation microscopy (PALM/STORM/PAINT etc ...). The package is multi platform, running on Windows, Linux, and OSX.

Get PYME or read the documentation.


Data Acquisition - PYMEAcquire

PYME offers a data acquisition module which performs the microscope and camera control functionality similar to that offered by e.g. micro-manager, but optimised for PALM/STORM type imaging. Some features include:

  • Support for a range of common hardware including Andor IXon and Neo cameras
  • Streaming of video to disk with on the fly compression and large (>4 GB) file size support
  • Customisable acquisition protocols.
  • Extensive meta-data capture.
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Real time distributed analysis infrastructure for PALM/STORM data

The real time analysis component allows analysis to be performed in real time, distributing the load across a small cluster if required.

  • Support for a range of different modalities (including 2D, 3D, & ratiometric multi-colour)
  • Weighted least squares fitting (as opposed to centroid based measures, although these are also available).
  • PSF type agnostic 3D fitting (using measured PSF)
  • Cluster clients run as standard programs on Win, Linux, and OSX
  • Cluster is dynamically scalable allowing nodes to be added while processing is taking place
  • Pluggable architecture allows new solvers to be added easily.
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PALM/STORM data exploration and visualisation tool

Offers a fast and flexible tool for exploring and visualising the list of fluorophore locations that is produced by PALM/STORM analysis algorithms.

  • OpenGL accelerated point cloud display
  • Points colourable by any fitted parameter (or parameters derived from these)
  • Filtering by fitted parameters or derived measures
  • Extensive support for ratiometric multi-colour datasets
  • Point chaining for single particle tracking or to collapse multiple localisations of a single fluorophore.
  • Multiple rendering options including Gaussian, histogram, and jittered triangulation.
  • Export as .tif or other standard image formats.
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Feature rich image viewer

A slice based image viewer for 2D, 3D, and 4D data sets, supporting many basic image processing tasks.

  • Widefield and confocal deconvolution.
  • Guided PSF extraction
  • Filtering, cropping and projections
  • Segmentation
  • Colocalisation and distance transforms
  • 3D isosurface & volume rendering
  • Data import and export
  • Vectorial chromatic shift calibration and correction
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Key Links