JaneliaSciComp/bigstream_deform
moduleApply local deformation (and optional affine) transforms to warp a moving image onto a fixed image using Bigstream
bigstream deformation warping 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 |
| fix_spacing | string | Voxel spacing for 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 |
| mov_spacing | string | Voxel spacing for the moving image |
| affine_transforms | file | One or more affine transformation files (paths to the corresponding affine.mat) |
| deform_dir | directory | Location of the displacement vector field |
| deform_subpath | string | Displacement vector subpath within the deform container |
| output_dir | directory | Output directory for the warped image |
| output_subpath | string | Subpath within the output container |
| output_timeindex | string | Time index for the output image |
| output_channel | string | Channel for the output image |
| 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 |
| fix_fullpath | string | Full resolved path to the fix image |
| fix_image_subpath | string | Subpath within the fix image container |
| mov_fullpath | string | Full resolved path to the moving image |
| mov_image_subpath | string | Subpath within the moving image container |
| output_fullpath | string | Full resolved path to the output warped image |
| output_subpath | string | Subpath within the output container |
Quick Start
Include this module in your Nextflow pipeline:
include { BIGSTREAM_DEFORM } from 'https://github.com/JaneliaSciComp/nextflow-modules/tree/main/modules/janelia/bigstream/deform'