Automated workflow for parallel Multiview Reconstruction

Type
Workflow
Author
Christopher Schmied
Peter Steinbach
Tobias Pietzsch
Stephan Preibisch
Pavel Tomancak
Requires
Fiji
Snakemake
Execution Platform
Linux
Supported image dimension
3D
multi-channel
time-series
Interaction Level
Automated
License/Openness
Free and open source
License
MIT
Description

Automated workflow for performing multiview reconstruction of large multiview, multichannel, multiillumination time-lapse SPIM data on a high performance computing (HPC) cluster or on a single workstation. 

has function
Image registration
Image deconvolution
Selective plane illumination microscopy reconstruction
Image processing
Drift correction
has topic
Light-sheet microscopy
Post date
03/25/2019 - 17:00
Last modified
05/24/2023 - 17:40
Workflow steps
Resave to hdf5
Conversion
Detection and Registration
Fiji
Image registration
Timelapse Registration
SPIM Registration Method (ImageJ)
Image registration
Multiview Deconvolution
Real-time multi-view deconvolution
Image deconvolution
Multiview Fusion
Fiji
Image processing
Download Page
https://github.com/mpicbg-scicomp/snakemake-workflows/tree/master/spim_registra…
Documentation Link
https://imagej.net/Automated_workflow_for_parallel_Multiview_Reconstruction
Reference Publication Link
https://academic.oup.com/bioinformatics/article/32/7/1112/1744153