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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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@@ -45,7 +45,7 @@ python3 auto_seg.py sliceloc segloc templateloc --bregma [coord]
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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 -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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```
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**Positional/Required Arguments**
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**Positional/Required Arguments**
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@@ -59,6 +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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|`--pdim [pixeldimensions]` |Dimensions of pixels, if not provided, these will be extracted from image metadata|
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-
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