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moving up docs about min size
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docs/do3d.rst

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@@ -60,6 +60,10 @@ is enabled, then the image will then be upsampled for finding the masks. This wi
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additional CPU and GPU memory, so for 3D you may want to set ``resample=False`` or in the CLI ``--no_resample``
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(more details here :ref:`resample`).
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3D segmentation ignores the ``flow_threshold`` because we did not find that
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it helped to filter out false positives in our test 3D cell volume. Instead,
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we found that setting ``min_size`` is a good way to remove false positives.
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There may be additional differences in YZ and XZ slices
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that make them unable to be used for 3D segmentation.
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I'd recommend viewing the volume in those dimensions if
@@ -80,7 +84,7 @@ Here is example code for a 3D stack with one channel (ZYX)
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with 3x less sampling in Z than in XY:
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::
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from cellpose import io, denoise, transforms
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io.logger_setup()
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img0 = io.imread("volume.tif")
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img_iso += img_iso2
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img_iso /= 2
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3D segmentation ignores the ``flow_threshold`` because we did not find that
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it helped to filter out false positives in our test 3D cell volume. Instead,
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we found that setting ``min_size`` is a good way to remove false positives.
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Training for 3D segmentation
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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