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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Contact us:

Whatever your experience with PYME, we want to hear from you! If you want to know if PYME will work for you we're happy to help. If you've run into problems we want to know so we can fix things. If you are a happy user, we also want to know as this helps us secure continued funding.

Get in touch with us at, connect with us on the forum using the "pyme" tag, or post an issue on our github repository.

Key Links