Nested-loop Ensemble PSF Fitting (NEP Fitting) is a method of simultaneously measuring image feature size and image resolution. The method is described in doi.org/10.1016/j.bpj.2018.07.028.
NEP-fitting is implemented as a plugin for the Python Microscopy Environment (PYME). PYME installation isntructions can be found at python-microscopy.org. Once installed, nep-fitting is accessible in the PYME image viewer (dh5view) by clicking 'sted_psf_fitting' in the modules drop-down menu.
The plugin itself can be installed via conda (general use) or from source (use and software development).
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You may want to make sure conda is up to date, e.g.
conda update condaorconda update -n <your environment name> conda -
Run
conda install -c barentine nep-fitting -
Test installation by running
STEDFitter -
Alternatively, run
dh5viewopen an image, and select 'sted_psf_fitting' from the 'modules' drop-down menu.
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Clone this repository
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python nep-fitting/setup.py install -
python nep-fitting/install_plugin.py -
Test installation by running
dh5view, loading an image, and selecting 'sted_psf_fitting' from the 'modules' drop-down menu.
If something isn't working for you, you'd like to contribute, or have any questions about nep-fitting, please get in touch with us on the image.sc forum using the pyme tag.