cellpose-napari
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Published
20 hours ago •
MouseLand
MouseLand
cellpose-napari crashes when running segmentation on Mac
Hi,
I'm trying to run the cellpose-napari on MacOS v.11.7.2 with Intel Graphics and following versions:
cellpose==2.1.1
cellpose-naapri==0.1.5
napari==0.4.16
pyhton==3.9.13
As soon as I hit the "run segmentation" button I get ~/envs/napari/bin/pythonw: line 3: 7607 Segmentation fault: 11 ~/envs/napari/python.app/Contents/MacOS/python "$@"
Is this expected behaviour? Do I need to change my versions? I saw something similar on the closed issues, but that was more than a year ago, not sure what the latest is?
Thanks, Christina
Running into the same issue here with an M1 Mac.
cellpose 2.2.2
cellpose-napari 0.1.5
napari 0.4.18
python 3.10.0
Not seeing any output in the Terminal, even with verbose turned on via running napari -v . Everything crashes when hitting Run segmentation
Not sure if I'm getting the same thing, but I get a hard crash with PyQt6 (6.5.1 and 6.6.1 from pip) while pyqt5 (conda-forge) is fine. Here's the log:
*** Terminating app due to uncaught exception 'NSRangeException', reason: '*** -[__NSArrayM objectAtIndexedSubscript:]: index 0 beyond bounds for empty array'
*** First throw call stack:
(
0 CoreFoundation 0x000000018881a800 __exceptionPreprocess + 176
1 libobjc.A.dylib 0x0000000188311eb4 objc_exception_throw + 60
2 CoreFoundation 0x0000000188790fc0 -[__NSCFString hasSuffix:] + 0
3 libqcocoa.dylib 0x000000016bfaa044 _ZN20QCocoaSystemTrayIcon13emitActivatedEv + 274796
4 libqcocoa.dylib 0x000000016bfaa0c8 _ZN20QCocoaSystemTrayIcon13emitActivatedEv + 274928
5 libqcocoa.dylib 0x000000016bfa8688 _ZN20QCocoaSystemTrayIcon13emitActivatedEv + 268208
6 QtWidgets 0x000000016c7a51a8 _ZN9QListView16selectionChangedERK14QItemSelectionS2_ + 204
7 QtWidgets.abi3.so 0x0000000169a0cfa4 _ZN12sipQListView16selectionChangedERK14QItemSelectionS2_ + 272
8 QtCore 0x000000016574f48c _ZN11QMetaObject8activateEP7QObjectPKS_iPPv + 3808
9 QtCore 0x0000000165915e44 _ZN19QItemSelectionModel20emitSelectionChangedERK14QItemSelectionS2_ + 216
10 QtCore 0x0000000165915a2c _ZN19QItemSelectionModel6selectERK14QItemSelection6QFlagsINS_13SelectionFlagEE + 636
11 QtCore 0x000000016591570c _ZN19QItemSelectionModel6selectERK11QModelIndex6QFlagsINS_13SelectionFlagEE + 68
12 QtCore 0x00000001659168cc _ZN19QItemSelectionModel15setCurrentIndexERK11QModelIndex6QFlagsINS_13SelectionFlagEE + 260
13 QtWidgets 0x000000016c603338 _ZNK9QComboBox5countEv + 828
14 QtWidgets 0x000000016c6068b4 _ZN9QComboBoxC1ER16QComboBoxPrivateP7QWidget + 2412
15 QtCore 0x000000016574f224 _ZN11QMetaObject8activateEP7QObjectPKS_iPPv + 3192
16 QtCore 0x00000001658fe944 _ZN18QAbstractItemModel13endInsertRowsEv + 200
17 QtGui 0x000000016a3e37a4 _ZN18QStandardItemModel11itemChangedEP13QStandardItem + 2376
18 QtWidgets 0x000000016c609910 _ZN9QComboBox10insertItemEiRK5QIconRK7QStringRK8QVariant + 368
19 QtWidgets.abi3.so 0x0000000169ba8904 _ZL22meth_QComboBox_addItemP7_objectS0_S0_ + 256
20 python3.10 0x00000001041a6b3c cfunction_call + 80
21 python3.10 0x000000010415359c _PyObject_MakeTpCall + 612
22 python3.10 0x00000001042455d8 call_function + 676
23 python3.10 0x0000000104240e60 _PyEval_EvalFrameDefault + 24940
24 python3.10 0x000000010423a364 _PyEval_Vector + 2036
25 python3.10 0x0000000104156c64 method_vectorcall + 172
26 python3.10 0x0000000104245540 call_function + 524
27 python3.10 0x0000000104240e60 _PyEval_EvalFrameDefault + 24940
28 python3.10 0x000000010423a364 _PyEval_Vector + 2036
29 python3.10 0x0000000104153850 _PyObject_FastCallDictTstate + 320
30 python3.10 0x0000000104154454 _PyObject_Call_Prepend + 176
31 python3.10 0x00000001041cb394 slot_tp_init + 116
32 python3.10 0x00000001041c3d64 type_call + 456
33 python3.10 0x000000010415359c _PyObject_MakeTpCall + 612
34 python3.10 0x00000001042455d8 call_function + 676
35 python3.10 0x00000001042413bc _PyEval_EvalFrameDefault + 26312
36 python3.10 0x000000010423a364 _PyEval_Vector + 2036
37 python3.10 0x0000000104245540 call_function + 524
38 python3.10 0x00000001042413bc _PyEval_EvalFrameDefault + 26312
39 python3.10 0x000000010423a364 _PyEval_Vector + 2036
40 python3.10 0x0000000104156c64 method_vectorcall + 172
41 python3.10 0x0000000104245540 call_function + 524
42 python3.10 0x00000001042413bc _PyEval_EvalFrameDefault + 26312
43 python3.10 0x000000010423a364 _PyEval_Vector + 2036
44 python3.10 0x0000000104245540 call_function + 524
45 python3.10 0x0000000104240e38 _PyEval_EvalFrameDefault + 24900
46 python3.10 0x000000010423a364 _PyEval_Vector + 2036
47 python3.10 0x00000001041537ac _PyObject_FastCallDictTstate + 156
48 python3.10 0x0000000104154454 _PyObject_Call_Prepend + 176
49 python3.10 0x00000001041c9ee0 slot_tp_call + 116
50 python3.10 0x000000010415359c _PyObject_MakeTpCall + 612
51 python3.10 0x00000001042455d8 call_function + 676
52 python3.10 0x0000000104241430 _PyEval_EvalFrameDefault + 26428
53 python3.10 0x000000010423a364 _PyEval_Vector + 2036
54 python3.10 0x0000000104156c64 method_vectorcall + 172
55 python3.10 0x0000000104245540 call_function + 524
56 python3.10 0x0000000104240e60 _PyEval_EvalFrameDefault + 24940
57 python3.10 0x000000010423a364 _PyEval_Vector + 2036
58 python3.10 0x0000000104156c64 method_vectorcall + 172
59 python3.10 0x0000000104245540 call_function + 524
60 python3.10 0x0000000104240e60 _PyEval_EvalFrameDefault + 24940
61 python3.10 0x000000010423a364 _PyEval_Vector + 2036
62 python3.10 0x0000000104245540 call_function + 524
63 python3.10 0x0000000104240e38 _PyEval_EvalFrameDefault + 24900
64 python3.10 0x000000010423a364 _PyEval_Vector + 2036
65 python3.10 0x0000000104245540 call_function + 524
66 python3.10 0x0000000104240e38 _PyEval_EvalFrameDefault + 24900
67 python3.10 0x000000010423a364 _PyEval_Vector + 2036
68 python3.10 0x0000000104153de0 PyVectorcall_Call + 156
69 python3.10 0x0000000104241658 _PyEval_EvalFrameDefault + 26980
70 python3.10 0x000000010423a364 _PyEval_Vector + 2036
71 python3.10 0x0000000104156c64 method_vectorcall + 172
72 python3.10 0x0000000104153de0 PyVectorcall_Call + 156
73 python3.10 0x0000000104241658 _PyEval_EvalFrameDefault + 26980
74 python3.10 0x000000010423a364 _PyEval_Vector + 2036
75 python3.10 0x00000001041537ac _PyObject_FastCallDictTstate + 156
76 python3.10 0x0000000104154454 _PyObject_Call_Prepend + 176
77 python3.10 0x00000001041c9ee0 slot_tp_call + 116
78 python3.10 0x000000010415359c _PyObject_MakeTpCall + 612
79 python3.10 0x00000001042455d8 call_function + 676
80 python3.10 0x0000000104241430 _PyEval_EvalFrameDefault + 26428
81 python3.10 0x000000010423a364 _PyEval_Vector + 2036
82 python3.10 0x0000000104245540 call_function + 524
83 python3.10 0x00000001042413bc _PyEval_EvalFrameDefault + 26312
84 python3.10 0x000000010423a364 _PyEval_Vector + 2036
85 QtCore.abi3.so 0x0000000165443208 _ZNK8PyQtSlot4callEP7_objectS1_ + 68
86 QtCore.abi3.so 0x000000016544309
libc++abi: terminating due to uncaught exception of type NSException
arm64 Sonoma python 3.10 cellpose 2.2.3 torch 2.1.1 napari 0.4.18
going to close this issue due to inactivity, napari does support pyqt6 on windows and linux without issues so maybe this is resolved
also cellpose now supports mac MPS acceleration, please upgrade to the latest version and also use pytorch>=2.4
if this still isn't working I'll reopen the issue
