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Commit 9a094bcc authored by Kai Schleicher's avatar Kai Schleicher
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Don't use z-slice option, input is a MIP

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2d_spots_in_fibers.py
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...@@ -765,7 +765,7 @@ canvas.close() ...@@ -765,7 +765,7 @@ canvas.close()
fiber_label_imp.show() fiber_label_imp.show()
# threshold DAPI channel and convert to binary # threshold DAPI channel and convert to binary
dapi_channel = BFopen_image(path_to_image, dapi_channel_number, series_number, z_slice_number=dapi_channel_zslice) dapi_channel = BFopen_image(path_to_image, dapi_channel_number, series_number)
if threshold <= 0: if threshold <= 0:
threshold = get_threshold_from_method(dapi_channel, "otsu") threshold = get_threshold_from_method(dapi_channel, "otsu")
dapi_binary = convert_to_binary(dapi_channel, threshold) dapi_binary = convert_to_binary(dapi_channel, threshold)
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