B6_dapi_template/automatic_segmentation_program/README.md

Output

Running the runner.py will yield the following outputs.

• A nifti file of the pre-processed input slice, called [outputdir]/[name].nii
• A directory with the same name as the input slice, [outputdir]/[name]/ in which you will find the following outputs
  • The different channels of the input slice ('im_c1.nii', 'im_c2.nii, ...')
  • The segmentation of the input file in pre-processed space, called Segmentation.nii (Can be viewed in ITK-SNAP by opening one of the channels as main image and the 'Segmentation.nii' as segmentation)
  • The DAPI template slice registered to the input slice, called TemplateSlice__InverseWarped.nii.gz
  • The input slice registered registered to the DAPI template slice, called im_c[dapi_index]_template.nii
  • The composite transformation of the input slice to the corresponding template slice, called 'Transformation_Composite.h5'
  • The inverse composite transformation, i.e. the transformation from the template slice to the input slice, called 'Transformation_InverseComposite.h5'

Parameters

Detailed parameter description. For example see ../Example/runner_example.sh

Usage

python3 runner.py sliceloc segloc templateloc bregma outputdir

Positional/Required Arguments

sliceloc	Location of the slice you wish to register (.nii or.nii.gz)
segloc	Location of file containing segmentation of the template (.nii or.nii.gz)
templateloc	Location of template file (.nii or .nii.gz)
bregma [coord]	Bregma coordinate of input slice
outputdir	Location for the output of the registration files

Optional arguments

--dapi [index]	Index of the DAPI channel in the slice, by default the DAPI channel is assumed to be the last channel