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Raise more informative error message when data with a large z-spacing is used #359

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Jan 10, 2024
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Raise more informative error message when data with a large z-spacing is used #359

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10 changes: 10 additions & 0 deletions cellfinder/core/detect/detect.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,16 @@ def calculate_parameters_in_pixels(
ball_xy_size = int(round(ball_xy_size_um / mean_in_plane_pixel_size))
ball_z_size = int(round(ball_z_size_um / float(voxel_sizes[0])))

if ball_z_size == 0:
raise ValueError(
"Ball z size has been calculated to be 0 voxels."
" This may be due to large axial spacing of your data or the "
"ball_z_size_um parameter being too small. "
"Please check input parameters are correct. "
"Note that cellfinder requires high resolution data in all "
"dimensions, so that cells can be detected in multiple "
"image planes."
)
return soma_diameter, max_cluster_size, ball_xy_size, ball_z_size


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