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fix readme formatting
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README.md

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@@ -94,19 +94,21 @@ folderpath = 'examples/example_brain/GLTa/'
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#try with and without ensemble to find the model which best works for you
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#if you have section numbers included in the filename as _sXXX specify this :)
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Model.predict(folderpath, ensemble=True, section_numbers=True)
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#This is an optional stage if you have damaged sections, or hemibrains they may negatively effect the propagation for the entire dataset
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#simply set the bad sections here using a string which is unique to those each section you would like to label as bad. DeepSlice will
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#not include it in the propagation and instead it will infer its position based on neighbouring sections.
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#This is an optional stage if you have damaged sections, or hemibrains they may negatively effect the
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#propagation for the entire dataset simply set the bad sections here using a string which is unique to
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#those each section you would like to label as bad. DeepSlice will not include it in the propagation
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#and instead it will infer its position based on neighbouring sections.
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Model.set_bad_sections(bad_sections=["_s094", "s199"])
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#If you would like to normalise the angles (you should)
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Model.propagate_angles()
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#To reorder your sections according to the section numbers
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Model.enforce_index_order()
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#alternatively if you know the precise spacing (ie; 1, 2, 4, indicates that section 3 has been left out of the series) Then you can use
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#alternatively if you know the precise spacing (ie; 1, 2, 4, indicates that section 3 has been left out.
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#Furthermore if you know the exact section thickness in microns this can be included instead of None
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#if your sections are numbered rostral to caudal you will need to specify a negative section_thickness
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Model.enforce_index_spacing(section_thickness = None)
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#now we save which will produce a json file which can be placed in the same directory as your images and then opened with QuickNII.
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#now we save which will produce a json file which can be placed in the same directory as your images and
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#then opened with QuickNII.
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Model.save_predictions(folderpath + 'MyResults')
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