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.
PYME offers a data acquisition module which performs the microscope and
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.
Real time distributed
analysis infrastructure for PALM/STORM data
The real time analysis component allows analysis to be performed in real time, distributing
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
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.
data exploration and
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
Multiple rendering options including Gaussian, histogram, and jittered triangulation.
Export as .tif or other standard image formats.
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
Colocalisation and distance transforms
3D isosurface & volume rendering
Data import and export
Vectorial chromatic shift calibration and correction
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.