Skip to content

make merging cells faster #1433

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
Turu-Tamas wants to merge 2 commits into
base: main
Choose a base branch
from
+11 −3
Open

make merging cells faster #1433

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
1befdc1
make merging cells faster
Turu-Tamas Apr 12, 2026
05a9a9b
non-buggy outlines
Turu-Tamas Apr 12, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
14 changes: 11 additions & 3 deletions cellpose/gui/gui.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1202,15 +1202,23 @@ def merge_cells(self, idx):
for z in range(self.NZ):
ar0, ac0 = np.nonzero(self.cellpix[z] == self.prev_selected)
ar1, ac1 = np.nonzero(self.cellpix[z] == self.selected)
touching = np.logical_and((ar0[:, np.newaxis] - ar1) < 3,
(ac0[:, np.newaxis] - ac1) < 3).sum()
ar = np.hstack((ar0, ar1))
ac = np.hstack((ac0, ac1))
vr0, vc0 = np.nonzero(self.outpix[z] == self.prev_selected)
vr1, vc1 = np.nonzero(self.outpix[z] == self.selected)
cell0 = set(zip(ar0, ac0))
outline1 = set(zip(vr1, vc1))
#touching = cell0.intersection(outline1)
pixels0 = set(zip(ar0, ac0))
touching = any(
(r0, c0) in pixels0
for r1, c1 in zip(ar1, ac1)
for r0 in range(r1 - 2, r1 + 3)
for c0 in range(c1 - 2, c1 + 3)
)
self.outpix[z, vr0, vc0] = 0
self.outpix[z, vr1, vc1] = 0
if touching > 0:
if touching:
mask = np.zeros((np.ptp(ar) + 4, np.ptp(ac) + 4), np.uint8)
mask[ar - ar.min() + 2, ac - ac.min() + 2] = 1
contours = cv2.findContours(mask, cv2.RETR_EXTERNAL,
Expand Down