# 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](http://www.itksnap.org/pmwiki/pmwiki.php) 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``` ](../Example/runner_example.sh)

**Usage**
```sh  
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|