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 super-resolution techniques (PALM/STORM/PAINT etc ...). The package is multi platform, running on Windows, Linux, and OSX.
Get PYME or read the documentation.
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:
The combination of high frame rates and large file sizes produced by modern microscopy experiments can easily overwhelm local storage. PYME offers a distributed storage system which allows microscope data to be compressed in real time and streamed in parallel to multiple storage nodes as it is acquired. Our system is designed to operate on inexpensive consumer-grade commodity hardware, whilst being scalable to 100s of TB of attached storage and GB/s of streaming bandwidth.
Allows complex data processing workflows to be defined without writing code by assembling pre-defined processing modules. The recipe specification removes allows reproducible workflows which can be run both locally and distributed across a cluster.
Our distributed analysis infrastructure allows scalable distribution of both single-molecule localization and more conventional image processing and quantification tasks. It can be used on a single-computer to divide processing between multiple cores, on HPC systems, or across a cluster of commodity computers.
Offers a fast and flexible tool for exploring and visualising the list of fluorophore locations that is produced by PALM/STORM analysis algorithms.
A slice based image viewer for 2D, 3D, and 4D data sets, supporting many basic image processing tasks.
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 support@python-microscopy.org, connect with us on the image.sc forum using the "pyme" tag, or post an issue on our github repository.