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@@ -1,4 +1,4 @@
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- # Description
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+# Description
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This repository contains the full data set for constructing the DAPI template, the full DAPI template creation pipeline and the automatic slice segmentation.
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This repository contains the full data set for constructing the DAPI template, the full DAPI template creation pipeline and the automatic slice segmentation.
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# Automatic slice segmentation
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# Automatic slice segmentation
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@@ -20,7 +20,10 @@ Program for automatic segmentation to a DAPI-stained coronal mouse brain slices.
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* Use preprocess.py to prepare input slice for automatic registration
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* Use preprocess.py to prepare input slice for automatic registration
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* Use auto_seg.py with preprocessed slice which will output a folder containing segmentation registered to slice.
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* Use auto_seg.py with preprocessed slice which will output a folder containing segmentation registered to slice.
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-## auto_seg.py
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+## Details
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+Detailed parameter description.
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+
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+### auto_seg.py
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**Usage**
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**Usage**
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```sh
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```sh
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python3 auto_seg.py sliceloc segloc templateloc --bregma [coord]
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python3 auto_seg.py sliceloc segloc templateloc --bregma [coord]
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@@ -42,7 +45,7 @@ python3 auto_seg.py sliceloc segloc templateloc --bregma [coord]
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|`--out [directory]` |Provide an alternative output directory (default directory is /output) |
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|`--out [directory]` |Provide an alternative output directory (default directory is /output) |
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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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|`--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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-## preprocess.py
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+### preprocess.py
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**Usage**
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**Usage**
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```sh
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```sh
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python3 preprocess.py file dir -s Series --pdim [pixeldimensions]
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python3 preprocess.py file dir -s Series --pdim [pixeldimensions]
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