Simplified scripts and added examples, please take a look at
org/fairsim/fiji/StepByStep.java (for Java)
scripts/ImageJ-reconstruction.bsh (for Beanshell)
This release also includes focal plane 5 from the test datasets for easy testing of the scripts. Just open the TIFF in ImageJ and run the beanshell script.
The script needs at least v.1.4.0 (this release) to work, as some additions where made to simplify it.
Added two features to deal with less-than-ideal data:
Image correction tab: Allows for rudimentary corrections of intensity variations between angles and phases.
Parameter estimation warning: A window will open with parameter estimation results (modulation depth estimations) and some guides how to interpret these.
fairSIM will now connect to standard JTransforms (3.1), additionally to shipping its own fork.
The maven build will only build against JTransforms, the makefile can use both.
This version adds (preliminary) support for Richardson-Lucy-based filtering.
See their publication for more detail.
To enable the feature, use the "settings" menu for the reconstruction.
- Small bugfix in test script
- GUI allows to select a single angle for reconstruction (beware: the resolution will not be isotropic, thus the apodization filter will not be ideal)
Initial release of the source code.
Code version from 2015-10-16, latest version available to the reviewers of the fairSIM publication.