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Readme for automatic_segmentation_program

Frederik Filip Stæger 4 年 前
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+# 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/``` ](../Example)
+
+**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|