JaneliaSciComp/bigstream_localalign
moduleLocal deformable alignment of a 3-D volume using Bigstream
bigstream local-alignment deformable-registration
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 fixed (reference) image (container) |
| fix_image_subpath | string | If the fix image is a zarr container this is the relative path to the dataset |
| fix_timeindex | string | Time index to select from the fix image |
| fix_channel | string | Channel to select from the fix image |
| mov_image | file|directory | Path to the moving image (container) |
| mov_image_subpath | string | If the moving image is a zarr container this is the relative path to the dataset |
| mov_timeindex | string | Time index to select from the moving image |
| mov_channel | string | Channel to select from the moving image |
| fix_mask | file|directory | Path to the mask for the fixed 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 moving image |
| mov_mask_subpath | string | If the moving mask is a zarr container this is the relative path to the mask dataset |
| affine_transform | file | Global affine transformation file |
| steps | string | Comma delimited list of the local alignment steps |
| transform_dir | directory | Output directory for the local transform |
| transform_name | string | Name of the local deformation transform file |
| transform_subpath | string | Subpath for the local deformation transform |
| inv_transform_name | string | Name of the inverse local deformation transform file |
| inv_transform_subpath | string | Subpath for the inverse local deformation transform |
| align_dir | directory | Output directory for the aligned (warped) image |
| align_name | string | Name of the locally aligned image file |
| align_subpath | string | Subpath for the aligned image |
| align_timeindex | string | Time index for the aligned output image |
| align_channel | string | Channel for the aligned output image |
| bigstream_config | file | Bigstream pipeline YAML configuration file |
| dask_scheduler | string | Dask scheduler address |
| dask_config | file | Dask configuration file (optional) |
| cpus | integer | Number of CPUs allocated to the process |
| mem_gb | integer | Memory in GB allocated to the process |
Outputs
| Name | Type | Description |
|---|---|---|
| meta | map | Groovy map containing: id |
| full_fix_image | string | Full resolved path to the fix image |
| fix_image_subpath | string | Subpath within the fix image container |
| full_mov_image | string | Full resolved path to the moving image |
| mov_image_subpath | string | Subpath within the moving image container |
| full_affine_transform | string | Full resolved path to the affine transform |
| full_transform_dir | string | Full resolved path to the transform directory |
| transform_name | string | Name of the local deformation transform file |
| transform_subpath | string | Subpath for the local deformation transform (defaults to mov_image_subpath if not provided) |
| inv_transform_name | string | Name of the inverse local deformation transform file |
| inv_transform_subpath | string | Subpath for the inverse local deformation transform |
| full_align_dir | string | Full resolved path to the aligned output directory |
| align_name | string | Name of the locally aligned image file |
| align_subpath | string | Subpath for the aligned image |
Quick Start
Include this module in your Nextflow pipeline:
include { BIGSTREAM_LOCALALIGN } from 'https://github.com/JaneliaSciComp/nextflow-modules/tree/main/modules/janelia/bigstream/localalign'