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Merged
merged 2 commits into from
Oct 22, 2024
Merged

Dev clean, updated notebook and bug fixes #27

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b32a71b
bug fix localmax detection
sebastiantiesmeyer Oct 22, 2024
c981500
updated Xenium notebook with newest syntax, names and comments;
sebastiantiesmeyer Oct 22, 2024
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444 changes: 215 additions & 229 deletions docs/source/tutorials/xenium_brain.ipynb
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2 changes: 1 addition & 1 deletion ovrlpy/_ovrlp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1468,7 +1468,7 @@ def run(

print("Running vertical adjustment")
_assign_xy(df)
_assign_z_mean_message_passing(df, rounds=4)
_assign_z_mean_message_passing(df, rounds=20)

vis = Visualizer(
KDE_bandwidth=KDE_bandwidth,
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5 changes: 4 additions & 1 deletion ovrlpy/_utils.py
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Expand Up @@ -78,7 +78,10 @@ def _determine_localmax_and_sample(distribution, min_distance=3, min_expression=

"""

rois_x, rois_y = find_local_maxima(distribution, min_distance, min_expression)
rois = find_local_maxima(distribution, min_distance, min_expression)

rois_x = rois[:, 0]
rois_y = rois[:, 1]

return rois_x, rois_y, distribution[rois_x, rois_y]

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