JaneliaSciComp/bigstream_globalalign
moduleGlobal affine alignment of a 3-D volume using Bigstream
affine registration bigstream
Module Information
Tools
bigstream
Tool for creating an alignment pipeline using different ITK algorithms
License: ['BSD-3-Clause']
Inputs
| Name | Type | Description |
|---|---|---|
| meta | map | Groovy map containing: id |
| fix_image | file|directory | Path to the low resolution fix (reference) image (container) |
| fix_image_subpath | string | If the fix image is a zarr container this is the relative path to the low resolution fix dataset |
| mov_image | file|directory | Path to the low resolution moving image (container) |
| mov_image_subpath | string | If the moving image is a zarr container this is the relative path to the moving dataset |
| fix_mask | file|directory | Path to the mask for the low resolution fix image |
| fix_mask_subpath | string | If the fix mask is a zarr container this is the relative path to the mask dataset |
| mov_mask | file|directory | Path to the mask for the low resolution moving image |
| mov_mask_subpath | string | If the moving mask is a zarr container this is the relative path to the mask dataset |
| steps | string | Comma delimmited list of the global alignment steps |
| output_dir | directory | Output directory |
| transform_name | string | Name of the file containing the affine transformation |
| alignment_name | string | Name of the affine transformed moving image |
| bigstream_config | file | bigstream pipeline yaml configuration file |
Quick Start
Include this module in your Nextflow pipeline:
include { BIGSTREAM_GLOBALALIGN } from 'https://github.com/JaneliaSciComp/nextflow-modules/tree/main/modules/janelia/bigstream/globalalign'