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lines changed Original file line number Diff line number Diff line change @@ -60,6 +60,10 @@ is enabled, then the image will then be upsampled for finding the masks. This wi
6060additional CPU and GPU memory, so for 3D you may want to set ``resample=False `` or in the CLI ``--no_resample ``
6161(more details here :ref: `resample `).
6262
63+ 3D segmentation ignores the ``flow_threshold `` because we did not find that
64+ it helped to filter out false positives in our test 3D cell volume. Instead,
65+ we found that setting ``min_size `` is a good way to remove false positives.
66+
6367There may be additional differences in YZ and XZ slices
6468that make them unable to be used for 3D segmentation.
6569I'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)
8084with 3x less sampling in Z than in XY:
8185
8286::
83-
87+
8488 from cellpose import io, denoise, transforms
8589 io.logger_setup()
8690 img0 = io.imread("volume.tif")
@@ -108,10 +112,6 @@ with 3x less sampling in Z than in XY:
108112 img_iso += img_iso2
109113 img_iso /= 2
110114
111- 3D segmentation ignores the ``flow_threshold `` because we did not find that
112- it helped to filter out false positives in our test 3D cell volume. Instead,
113- we found that setting ``min_size `` is a good way to remove false positives.
114-
115115Training for 3D segmentation
116116~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
117117
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