This repository contains pipeline code for handling AIC's LLSM and MOSAIC data. The pipeline consists of multiple discrete modules: cropping, deskewing, deconvolution, and maximum intensity projection. The pipeline is accessed via the command line using the llsm-pipeline and mosaic-pipeline commands.
For most cases, the llsm-pipeline and mosaic-pipeline commands should be all that is needed. However, the individual modules, which each compile to a separate binary, can be run directly on a single file if needed. Use the -h option with any command to get a list of supported arguments.
For more information on each module, information on dependencies and installation, and example commands, see the documentation at https://aicjanelia.github.io/LLSM/.
The pipeline is initiated by calling the llsm-pipeline or mosaic-pipeline command and providing it with a properly formatted config.json file. See an example configuration file here. We recommend using the --dry-run command to check your pipeline run before submitting jobs to the cluster.
llsm-pipeline /aic/instruments/llsm/experimentFolder/config.json
mosaic-pipeline /aic/instruments/MOSAIC/experimentFolder/config.json
| Microscope | Angle | μm/pixel |
|---|---|---|
| LLSM | 31.8° | 0.104 |
| MOSAIC | -32.45° = 147.55° | 0.108 |
usage: llsm-pipeline [-h] [--dry-run] [--verbose] input
Batch deskewing, deconvolution, and mip script for LLSM images.
positional arguments:
input path to configuration JSON file
optional arguments:
-h, --help show this help message and exit
--dry-run, -d execute without submitting any bsub jobs
--verbose, -v print details (including commands to bsub)