PySIMRecon

Easy to use wrapper for pyCUDAsirecon, allowing the use of DV (DeltaVision) files without IVE/Priism (UCSF library with MRC/DV support).

This is built for easy use from the command line or as part of an auto-processing pipeline, allowing parameters to be pre-configured or defined at runtime.

Goal

To reconstruct the SIM data and create OTFs from PSFs from the cryoSIM at B24, Diamond from the .dv files created by Cockpit. Requirements are:

• Easy to use
• Open source
• Reproducable results
• Can be used as part of an automatic processing pipeline

Current state

Under development

Configuration

Calls to sim-otf and sim-recon can both take a -c/--config argument. This should be similar to the config.ini file in the configs directory, which specifies the defaults config, any per-channel configs (some values should be set on a per-channel basis), and the locations of OTFs for each channel. The channels are specified based on the emission wavelength in nanometres (must be an integer).

Example:

For a channel with an emission wavelength of 525nm:

• In the [configs] section, the channel config can be specified as 525=/path/to/configs/525.cfg
• In the [otfs] section, the channel OTF file can be specified as 525=/path/to/otfs/525_otf.tiff A directory can be specified within each of the [configs] and [otfs] sections. If given, files can also be defined relative to that directory, e.g. if directory=/path/to, then 525=/path/to/otfs/525_otf.tiff could simply be 525=otfs/525_otf.tiff. Config settings will be overriden by higher-priority sources.

Order of setting priority:

1. Command line arguments (override all)
2. Per-channel configs (override defaults for the appropriate channel only)
3. Defaults (override any cudasirecon defaults)