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+# Output
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+Running the runner.py will yield the following outputs.
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+ - A nifti file of the pre-processed input slice, called ```[outputdir]/[name].nii```
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+ - A directory with the same name as the input slice, ```[outputdir]/[name]/``` in which you will find the following outputs
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+ - The different channels of the input slice ('im_c1.nii', 'im_c2.nii, ...')
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+ - 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)
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+ - The DAPI template slice registered to the input slice, called ```TemplateSlice__InverseWarped.nii.gz```
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+ - The input slice registered registered to the DAPI template slice, called ```im_c[dapi_index]_template.nii```
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+ - The composite transformation of the input slice to the corresponding template slice, called 'Transformation_Composite.h5'
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+ - The inverse composite transformation, i.e. the transformation from the template slice to the input slice, called 'Transformation_InverseComposite.h5'
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+
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+# Parameters
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+Detailed parameter description. For example see [```../Example/``` ](../Example)
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+
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+**Usage**
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+```sh
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+python3 runner.py sliceloc segloc templateloc bregma outputdir
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+```
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+
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+**Positional/Required Arguments**
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+
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+|||
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+|--------------------------------|-----------------------------|
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+|`sliceloc` |Location of the slice you wish to register (.nii or.nii.gz) |
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+|`segloc` |Location of file containing segmentation of the template (.nii or.nii.gz) |
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+|`templateloc`|Location of template file (.nii or .nii.gz)|
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+|`bregma [coord]`|Bregma coordinate of input slice |
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+|`outputdir`| Location for the output of the registration files|
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+**Optional arguments**
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+
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+| | |
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+|---|---|
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+|`--dapi [index]` |Index of the DAPI channel in the slice, by default the DAPI channel is assumed to be the last channel|
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