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@@ -1,7 +1,10 @@
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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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+
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+# Automatic slice segmentation
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+
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+Program for automatic segmentation to a DAPI-stained coronal mouse brain slices.
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-#Automatic slice segmentation
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-
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-Program for automatically registering a segmentation to a DAPI-stained slice.
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## Dependencies
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* Python 3.6
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@@ -33,8 +36,8 @@ python3 auto_seg.py sliceloc segloc templateloc --bregma [coord]
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**Optional arguments**
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-|||
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-|--------------------------------|-----------------------------|
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+| | |
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+|---|---|
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|`--approx [index]` |Provide the location of the slice as a z-index of the template. Can be used instead of --bregma argument.|
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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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@@ -42,7 +45,7 @@ python3 auto_seg.py sliceloc segloc templateloc --bregma [coord]
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## preprocess.py
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**Usage**
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```sh
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-python3 preprocess.py file dir -s Series -b [True/False] --pdim [pixeldimension]
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+python3 preprocess.py file dir -s Series --pdim [pixeldimensions]
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```
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**Positional/Required Arguments**
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@@ -56,6 +59,4 @@ python3 preprocess.py file dir -s Series -b [True/False] --pdim [pixeldimension]
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|--------------------------------|-----------------------------|
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-|`--b [True/False]` |Bias field correction: Whether to use bias-field correction in preprocessing (default: True)|
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|`--pdim [pixeldimensions]` |Dimensions of pixels, if not provided, these will be extracted from image metadata|
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-
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