Plugins and associated code for PYME (AKA python-microscopy).
This is a mixed bag of extensions/additions to standard PYME and also used as a testbed for
- the recipe based processing of SMLM data
- new ideas for data processing
Installation is achieved with
# cd to PYME-extra subdirectory
python setup.py install
python install_plugins.py dist
Alternatively, if you want to edit code in place you may want to use a development install
# cd to PYME-extra subdirectory
python setup.py develop
python install_plugins.py dist
For user installs, plugin files can be installed in the per user config directory by leaving out the dist argument to install_plugins.py:
python install_plugins.py
External modules required for full functionality are listed in requirements.txt, these currently include
python-microscopy
statsmodels # for FRC smoothing with the lowess filter
roifile # to allow using info from ImageJ/Fiji ROIs
colorcet # add some colorcet colour tables in PYME
circle-fit # needs pip install to get recent version; for 2D NPC analysis
Note that the showErrs modules rely on a mac installation which uses bash scripts and the platypus app app to capture STDERR into a temporary file which these modules access.
Bottom line is that these two error display modules will likely not work on anything but a mac with my PYMEapps wrappers. On other systems they will just generate a message that this functionality is not supported.
The PYME mac app wrappers are available at the PYME-apps repository.
Christian Soeller (c.soeller at gmail dot com)