Library for importing and dealing with data from the Utrecht University Soft Condensed Matter groups confocal microscopes, including some general utility functions.
The documentation can be found here
- created by: Maarten Bransen
- email: m.bransen@uu.nl
This package can be installed directly from GitHub using pip:
pip install git+https://github.com/UU-SCMB/scm_confocal
When using the Anaconda distribution, it is safer to run the conda version of pip as follows:
conda install pip
conda install git
pip install git+https://github.com/UU-SCMB/scm_confocal
To update to the most recent version, use pip install with the --upgrade flag set:
pip install --upgrade git+https://github.com/UU-SCMB/scm_confocal
The classes in this package typically require specific exporting formats from the confocal, and differ in specific implementation details because of this. I have attempted to be consistent in naming functions but each class has its own peculiarities based on personal need.
Data from the SP8 can be saved as the native .lif files and imported using the sp8_lif class, which is essentially a wrapper around the readlif library. This supports most (but not all) functions of the sp8, but development is ongoing.
Alternatively, data can be exported using the Leica LAS software (the microscope operation software), with the check marks for use RAW data checked, and these can be loaded using sp8_series with support for all functions of the sp8, provided that a full series is stored in its own folder together with a metadata folder. In principle data exported in color (so with a LUT applied) is accepted but not ideal and will return a warning for this reason.
Two classes are available:
- visitech_series for normal multy-dimensional acquisitions using MicroManager
- visitech_faststack for xyzt data recorded using our custom
faststackdriver, which bypasses the z-stage feedback loop and metadata in favor of acquisition speed.
Additionally, some utility functions for stacks on multidimensional microscopy data are included such as binning, rescaling, etc.