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change default handling for images with z-stacks
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run_batch_general.py

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Original file line numberDiff line numberDiff line change
@@ -84,7 +84,7 @@ def run_batch_general(
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"pipelinepath": posixpath.join(
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"projects", identifier, "workspace", "pipelines", batch
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),
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"zprojoutpath": posixpath.join("projects", identifier, batch, "images"),
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"zprojoutpath": posixpath.join("projects", identifier, batch, "images_projected"),
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"zprojoutputstructure": "Metadata_Plate",
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"illumoutpath": posixpath.join("projects", identifier, batch, "illum"),
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"QCoutpath": posixpath.join(

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