LLSM Processing Pipeline
The Advanced Imaging Center (AIC) uses this pipeline for pre-processing of images created on our LLSM or MOSAIC systems. The pipeline consists of multiple discrete modules that are accessed via the command line using either the llsm-pipeline or mosaic-pipeline commands. Which modules to implement are controlled by a configuration JSON file. The main difference in the two pipelines is the parsing of filenames and acquisition settings metadata.
Each of the modules compiles to a separate binary that can also be directly executed by calling it on the command line. These modules are:
- Flatfield Correction
- Cropping
- Deskewing
- Deconvolution
- Maximum Intensity Projection
The main pipeline command and each individual module are further described in this documentation. With any command, you can also use the -h option to get a list of supported arguments.
Cheatsheet
Command Line Examples
llsm-pipeline /aic/instruments/llsm/experimentFolder/config.json
mosaic-pipeline /aic/instruments/MOSAIC/experimentFolder/config.json
Configuration File
See an example configuration file here.
Microscope Parameters
| Microscope | Angle | μm/pixel |
|---|---|---|
| LLSM | 31.8° | 0.104 |
| MOSAIC | -32.45° = 147.55° | 0.108 |