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@@ -1,10 +1,7 @@
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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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@@ -36,8 +33,8 @@ 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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