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ClearAnatomics / ClearMap

ClearMap 2 with WobblyStitcher, TubeMap and CellMap
https://clearanatomics.github.io/ClearMapDocumentation/
GNU General Public License v3.0
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Wobbly Stitcher black tiles #54

Open ilangesa23 opened 3 years ago

ilangesa23 commented 3 years ago

Hi Christoph,

Thanks for all the work on this program and providing the documentation for it. I have been trying to use WobblyStitcher for cFos imaged brains. Whenever I stitch the sample, regardless of values I use for the validate or validate_slice variables (even really low minimum values and size values), I keep getting some fully black tiles in the stitched brain. Is there a way to fix this? Thanks in advance for the help.

ChristophKirst commented 3 years ago

Have you tried to setting the validation to None to see if that is actually causing the black tiles?

andrewsilberfeld commented 2 years ago

@ilangesa23 did you ever figure this out? I'm having a similar problem despite setting multiple parameters to "none". I'm not sure why this is happening.

stw.align_layout(layout, axis_range=(None, None, 3), max_shifts=[(-25,25),(-90,90),(-10,10)], axis_mip=None, validate=None, prepare=None, validate_slice=None, prepare_slice =None, find_shifts=dict(method='tracing', cutoff=3*np.sqrt(2)), processes=None, verbose=True);