CellProf quits unexpectedly during analysis - Mac OS 10.6

Hey,

I am working on a Macbook with OS 10.6.3 using CellProfiler v.9777 for Mac.
The pipeline construction works fine and running the pipeline also in the beginning
seems to be normal, all modules are conducted without any obvious error.
However, before the second image is processed ‘CellProfiler quit unexpectedly’.
And it always does this, meaning that I cannot generate an output file.

I’ve checked Console and the message I get is:
26.04.10 08:16:52 CellProfiler2.0[5983] Process manager already initialized – can’t fully enable headless mode.
26.04.10 08:17:01 com.apple.launchd.peruser.501[86] ([0x0-0x139139].org.pythonmac.unspecified.CellProfiler2.0[5983]) Job appears to have crashed: Bus error26.04.10 08:17:03 ReportCrash[6001] Saved crash report for CellProfiler2.0[5983] version Revision: 9719 (Revision: 9719 ) to /Users/name/Library/Logs/DiagnosticReports/CellProfiler2.0_2010-04-26-081703_name-MacBook.crash

I will post the error report in replies. (It’s too long and attachment don’t work as the file extensions are not allowed on the forum).
It would be great if someone could help me with this. I have no idea about coding or anything, but I need this
to work on my computer as resorting to my Windows machine is not really the greatest option.

Thanks a lot, Linda

The error report for Apple is:
Process: CellProfiler2.0 [6406]
Path: /Applications/CellProfiler2.0.app/Contents/MacOS/CellProfiler2.0
Identifier: org.pythonmac.unspecified.CellProfiler2.0
Version: Revision: 9719 (Revision: 9719 )
Code Type: X86 (Native)
Parent Process: launchd [86]

Date/Time: 2010-04-26 22:31:38.795 +0200
OS Version: Mac OS X 10.6.3 (10D573)
Report Version: 6

Interval Since Last Report: 456868 sec
Crashes Since Last Report: 12
Per-App Interval Since Last Report: 8389 sec
Per-App Crashes Since Last Report: 11
Anonymous UUID: B24D529D-9922-44F5-AE11-C2B9A5C9E756

Exception Type: EXC_BAD_ACCESS (SIGBUS)
Exception Codes: KERN_PROTECTION_FAILURE at 0x0000000017e122c1
Crashed Thread: 0 Dispatch queue: com.apple.main-thread

Thread 0 Crashed: Dispatch queue: com.apple.main-thread
0 ??? 0x1485100f 0 + 344264719
1 libawt.jnilib 0x66c8b51e NotBusyObserver + 18
2 com.apple.CoreFoundation 0x98b222e2 __CFRunLoopDoObservers + 1186
3 com.apple.CoreFoundation 0x98adec72 __CFRunLoopRun + 1154
4 com.apple.CoreFoundation 0x98ade0f4 CFRunLoopRunSpecific + 452
5 com.apple.CoreFoundation 0x98addf21 CFRunLoopRunInMode + 97
6 com.apple.HIToolbox 0x90ce40fc RunCurrentEventLoopInMode + 392
7 com.apple.HIToolbox 0x90ce3eb1 ReceiveNextEventCommon + 354
8 com.apple.HIToolbox 0x90e6c287 ReceiveNextEvent + 83
9 libwx_macud-2.8.0.dylib 0x133adbbe wxApp::MacDoOneEvent() + 84
10 libwx_macud-2.8.0.dylib 0x133c7fa6 wxEventLoop::Dispatch() + 32
11 libwx_macud-2.8.0.dylib 0x13482bed wxEventLoopManual::Run() + 97
12 libwx_macud-2.8.0.dylib 0x13459146 wxAppBase::MainLoop() + 76
13 core.so 0x13185774 wxPyApp::MainLoop() + 52
14 core.so 0x131d31f6 wxIntersectRect(wxRect*, wxRect*) + 220430
15 libpython2.5.dylib 0x00409dac PyObject_Call + 45
16 libpython2.5.dylib 0x004936e1 PyEval_EvalFrameEx + 14836
17 libpython2.5.dylib 0x0049671d PyEval_EvalCodeEx + 1819
18 libpython2.5.dylib 0x0042b103 PyFunction_SetClosure + 1919
19 libpython2.5.dylib 0x00409dac PyObject_Call + 45
20 libpython2.5.dylib 0x00411aa7 PyMethod_New + 2432
21 libpython2.5.dylib 0x00409dac PyObject_Call + 45
22 libpython2.5.dylib 0x00491577 PyEval_EvalFrameEx + 6282
23 libpython2.5.dylib 0x00495b86 PyEval_EvalFrameEx + 24217
24 libpython2.5.dylib 0x0049671d PyEval_EvalCodeEx + 1819
25 libpython2.5.dylib 0x004968d1 PyEval_EvalCode + 87
26 libpython2.5.dylib 0x004ba031 PyRun_FileExFlags + 260
27 libpython2.5.dylib 0x0048acad PyAST_FromNode + 7784
28 libpython2.5.dylib 0x00494acd PyEval_EvalFrameEx + 19936
29 libpython2.5.dylib 0x0049671d PyEval_EvalCodeEx + 1819
30 libpython2.5.dylib 0x00493d9e PyEval_EvalFrameEx + 16561
31 libpython2.5.dylib 0x0049671d PyEval_EvalCodeEx + 1819
32 libpython2.5.dylib 0x004968d1 PyEval_EvalCode + 87
33 libpython2.5.dylib 0x004ba031 PyRun_FileExFlags + 260
34 libpython2.5.dylib 0x004ba3cb PyRun_SimpleFileExFlags + 640
35 libpython2.5.dylib 0x004ba56e PyRun_SimpleFile + 40
36 …unspecified.CellProfiler2.0 0x00007b9f start + 23863
37 …unspecified.CellProfiler2.0 0x00008091 main + 297
38 …unspecified.CellProfiler2.0 0x00001f63 start + 251
39 …unspecified.CellProfiler2.0 0x00001e91 start + 41

Thread 1: Dispatch queue: com.apple.libdispatch-manager
0 libSystem.B.dylib 0x94e5db42 kevent + 10
1 libSystem.B.dylib 0x94e5e25c _dispatch_mgr_invoke + 215
2 libSystem.B.dylib 0x94e5d719 _dispatch_queue_invoke + 163
3 libSystem.B.dylib 0x94e5d4be _dispatch_worker_thread2 + 240
4 libSystem.B.dylib 0x94e5cf41 _pthread_wqthread + 390
5 libSystem.B.dylib 0x94e5cd86 start_wqthread + 30

Thread 2:
0 libSystem.B.dylib 0x94e37342 semaphore_wait_signal_trap + 10
1 libSystem.B.dylib 0x94e64eb8 _pthread_cond_wait + 1089
2 libSystem.B.dylib 0x94ead42f pthread_cond_wait + 48
3 libpython2.5.dylib 0x004c5029 PyThread_acquire_lock + 140
4 libpython2.5.dylib 0x004c9617 _PyObject_GC_Del + 217
5 libpython2.5.dylib 0x00494acd PyEval_EvalFrameEx + 19936
6 libpython2.5.dylib 0x0049671d PyEval_EvalCodeEx + 1819
7 libpython2.5.dylib 0x00493d9e PyEval_EvalFrameEx + 16561
8 libpython2.5.dylib 0x0049671d PyEval_EvalCodeEx + 1819
9 libpython2.5.dylib 0x00493d9e PyEval_EvalFrameEx + 16561
10 libpython2.5.dylib 0x0049671d PyEval_EvalCodeEx + 1819
11 libpython2.5.dylib 0x0042b103 PyFunction_SetClosure + 1919
12 libpython2.5.dylib 0x00409dac PyObject_Call + 45
13 libpython2.5.dylib 0x004936e1 PyEval_EvalFrameEx + 14836
14 libpython2.5.dylib 0x00495b86 PyEval_EvalFrameEx + 24217
15 libpython2.5.dylib 0x00495b86 PyEval_EvalFrameEx + 24217
16 libpython2.5.dylib 0x0049671d PyEval_EvalCodeEx + 1819
17 libpython2.5.dylib 0x0042b103 PyFunction_SetClosure + 1919
18 libpython2.5.dylib 0x00409dac PyObject_Call + 45
19 libpython2.5.dylib 0x00411aa7 PyMethod_New + 2432
20 libpython2.5.dylib 0x00409dac PyObject_Call + 45
21 libpython2.5.dylib 0x0048ee63 PyEval_CallObjectWithKeywords + 112
22 libpython2.5.dylib 0x004c9c73 _PyObject_GC_Del + 1845
23 libSystem.B.dylib 0x94e64a19 _pthread_start + 345
24 libSystem.B.dylib 0x94e6489e thread_start + 34

Thread 3: Java: Exception Handler Thread
0 libSystem.B.dylib 0x94e372fa mach_msg_trap + 10
1 libSystem.B.dylib 0x94e37a67 mach_msg + 68
2 libSystem.B.dylib 0x94ea3048 mach_msg_server + 520
3 libclient.dylib 0x18d7ae25 JNI_CreateJavaVM_Impl + 61045
4 libclient.dylib 0x18d7adca JNI_CreateJavaVM_Impl + 60954
5 libclient.dylib 0x18d7933b JNI_CreateJavaVM_Impl + 54155
6 libSystem.B.dylib 0x94e64a19 _pthread_start + 345
7 libSystem.B.dylib 0x94e6489e thread_start + 34

Thread 4: Java: Gang worker#0 (Parallel GC Threads)
0 libSystem.B.dylib 0x94e372fa mach_msg_trap + 10
1 libSystem.B.dylib 0x94e37a67 mach_msg + 68
2 libclient.dylib 0x18d79f23 JNI_CreateJavaVM_Impl + 57203
3 libclient.dylib 0x18d79dab JNI_CreateJavaVM_Impl + 56827
4 libclient.dylib 0x18d79928 JNI_CreateJavaVM_Impl + 55672
5 libclient.dylib 0x18d79588 JNI_CreateJavaVM_Impl + 54744
6 libclient.dylib 0x18d8f931 jio_vsnprintf + 321
7 libclient.dylib 0x18d8f86a jio_vsnprintf + 122
8 libclient.dylib 0x18d7933b JNI_CreateJavaVM_Impl + 54155
9 libSystem.B.dylib 0x94e64a19 _pthread_start + 345
10 libSystem.B.dylib 0x94e6489e thread_start + 34

Thread 5: Java: Gang worker#1 (Parallel GC Threads)
0 libSystem.B.dylib 0x94e372fa mach_msg_trap + 10
1 libSystem.B.dylib 0x94e37a67 mach_msg + 68
2 libclient.dylib 0x18d79f23 JNI_CreateJavaVM_Impl + 57203
3 libclient.dylib 0x18d79dab JNI_CreateJavaVM_Impl + 56827
4 libclient.dylib 0x18d79928 JNI_CreateJavaVM_Impl + 55672
5 libclient.dylib 0x18d79588 JNI_CreateJavaVM_Impl + 54744
6 libclient.dylib 0x18d8f931 jio_vsnprintf + 321
7 libclient.dylib 0x18d8f86a jio_vsnprintf + 122
8 libclient.dylib 0x18d7933b JNI_CreateJavaVM_Impl + 54155
9 libSystem.B.dylib 0x94e64a19 _pthread_start + 345
10 libSystem.B.dylib 0x94e6489e thread_start + 34

Thread 6: Java: Concurrent Mark-Sweep GC Thread
0 libSystem.B.dylib 0x94e372fa mach_msg_trap + 10
1 libSystem.B.dylib 0x94e37a67 mach_msg + 68
2 libclient.dylib 0x18d7a037 JNI_CreateJavaVM_Impl + 57479
3 libclient.dylib 0x18d96bb0 jio_vsnprintf + 29632
4 libclient.dylib 0x18d799b7 JNI_CreateJavaVM_Impl + 55815
5 libclient.dylib 0x18d79588 JNI_CreateJavaVM_Impl + 54744
6 libclient.dylib 0x18e53b8c JVM_Available + 29852
7 libclient.dylib 0x18d96992 jio_vsnprintf + 29090
8 libclient.dylib 0x18d7933b JNI_CreateJavaVM_Impl + 54155
9 libSystem.B.dylib 0x94e64a19 _pthread_start + 345
10 libSystem.B.dylib 0x94e6489e thread_start + 34

Thread 7: Java: VM Thread
0 libclient.dylib 0x18ece9dd JVM_ResolveClass + 24989
1 libclient.dylib 0x18e9d5d6 JVM_GC + 10918
2 libclient.dylib 0x1908cb51 JVM_RaiseSignal + 307697
3 libclient.dylib 0x18e9cdd1 JVM_GC + 8865
4 libclient.dylib 0x18e8ccd6 JVM_NanoTime + 18710
5 libclient.dylib 0x18e8ca55 JVM_NanoTime + 18069
6 libclient.dylib 0x18e8c8da JVM_NanoTime + 17690
7 libclient.dylib 0x18e9cd0d JVM_GC + 8669
8 libclient.dylib 0x18e9c377 JVM_GC + 6215
9 libclient.dylib 0x18e9bd0b JVM_GC + 4571
10 libclient.dylib 0x18e9b94f JVM_GC + 3615
11 libclient.dylib 0x18e9b557 JVM_GC + 2599
12 libclient.dylib 0x18e9b4f9 JVM_GC + 2505
13 libclient.dylib 0x18e89aa1 JVM_NanoTime + 5857
14 libclient.dylib 0x18e9afd4 JVM_GC + 1188
15 libclient.dylib 0x18e9af01 JVM_GC + 977
16 libclient.dylib 0x18e76207 JVM_EnableCompiler + 14471
17 libclient.dylib 0x18e76119 JVM_EnableCompiler + 14233
18 libclient.dylib 0x18e0f13b JVM_Lseek + 143243
19 libclient.dylib 0x18e0ec8a JVM_Lseek + 142042
20 libclient.dylib 0x18d7933b JNI_CreateJavaVM_Impl + 54155
21 libSystem.B.dylib 0x94e64a19 _pthread_start + 345
22 libSystem.B.dylib 0x94e6489e thread_start + 34

Thread 8: Java: Reference Handler
0 libSystem.B.dylib 0x94e372fa mach_msg_trap + 10
1 libSystem.B.dylib 0x94e37a67 mach_msg + 68
2 libclient.dylib 0x18d79f23 JNI_CreateJavaVM_Impl + 57203
3 libclient.dylib 0x18d79dab JNI_CreateJavaVM_Impl + 56827
4 libclient.dylib 0x18e23c95 JVM_MonitorWait + 5461
5 libclient.dylib 0x18e22bfe JVM_MonitorWait + 1214
6 libclient.dylib 0x18e2287a JVM_MonitorWait + 314
7 ??? 0x1a80b839 0 + 444643385
8 ??? 0x1a803db1 0 + 444612017
9 ??? 0x1a803db1 0 + 444612017
10 ??? 0x1a8012d3 0 + 444601043
11 libclient.dylib 0x18e107d0 JVM_Lseek + 149024
12 libclient.dylib 0x18e10576 JVM_Lseek + 148422
13 libclient.dylib 0x18e2211b JVM_InternString + 2123
14 libclient.dylib 0x18e21f8a JVM_InternString + 1722
15 libclient.dylib 0x18e21d74 JVM_InternString + 1188
16 libclient.dylib 0x18e2180f JVM_StartThread + 2175
17 libclient.dylib 0x18d7933b JNI_CreateJavaVM_Impl + 54155
18 libSystem.B.dylib 0x94e64a19 _pthread_start + 345
19 libSystem.B.dylib 0x94e6489e thread_start + 34

Thread 9: Java: Finalizer
0 libSystem.B.dylib 0x94e372fa mach_msg_trap + 10
1 libSystem.B.dylib 0x94e37a67 mach_msg + 68
2 libclient.dylib 0x18d79f23 JNI_CreateJavaVM_Impl + 57203
3 libclient.dylib 0x18d79dab JNI_CreateJavaVM_Impl + 56827
4 libclient.dylib 0x18e23c95 JVM_MonitorWait + 5461
5 libclient.dylib 0x18e22bfe JVM_MonitorWait + 1214
6 libclient.dylib 0x18e2287a JVM_MonitorWait + 314
7 ??? 0x1a80b839 0 + 444643385
8 ??? 0x1a803db1 0 + 444612017
9 ??? 0x1a803f17 0 + 444612375
10 ??? 0x1a803f17 0 + 444612375
11 ??? 0x1a8012d3 0 + 444601043
12 libclient.dylib 0x18e107d0 JVM_Lseek + 149024
13 libclient.dylib 0x18e10576 JVM_Lseek + 148422
14 libclient.dylib 0x18e2211b JVM_InternString + 2123
15 libclient.dylib 0x18e21f8a JVM_InternString + 1722
16 libclient.dylib 0x18e21d74 JVM_InternString + 1188
17 libclient.dylib 0x18e2180f JVM_StartThread + 2175
18 libclient.dylib 0x18d7933b JNI_CreateJavaVM_Impl + 54155
19 libSystem.B.dylib 0x94e64a19 _pthread_start + 345
20 libSystem.B.dylib 0x94e6489e thread_start + 34

Thread 10: Java: Surrogate Locker Thread (CMS)
0 libSystem.B.dylib 0x94e372fa mach_msg_trap + 10
1 libSystem.B.dylib 0x94e37a67 mach_msg + 68
2 libclient.dylib 0x18d79f23 JNI_CreateJavaVM_Impl + 57203
3 libclient.dylib 0x18d79dab JNI_CreateJavaVM_Impl + 56827
4 libclient.dylib 0x18d79928 JNI_CreateJavaVM_Impl + 55672
5 libclient.dylib 0x18d794a9 JNI_CreateJavaVM_Impl + 54521
6 libclient.dylib 0x18e39097 JVM_IsPrimitiveClass + 7639
7 libclient.dylib 0x18e38c11 JVM_IsPrimitiveClass + 6481
8 libclient.dylib 0x18e21d74 JVM_InternString + 1188
9 libclient.dylib 0x18e2180f JVM_StartThread + 2175
10 libclient.dylib 0x18d7933b JNI_CreateJavaVM_Impl + 54155
11 libSystem.B.dylib 0x94e64a19 _pthread_start + 345
12 libSystem.B.dylib 0x94e6489e thread_start + 34

Thread 11: Java: Signal Dispatcher
0 libSystem.B.dylib 0x94e37336 semaphore_wait_trap + 10
1 libclient.dylib 0x18e39b5e JVM_IsPrimitiveClass + 10398
2 libclient.dylib 0x18e3992e JVM_IsPrimitiveClass + 9838
3 libclient.dylib 0x18e21d74 JVM_InternString + 1188
4 libclient.dylib 0x18e2180f JVM_StartThread + 2175
5 libclient.dylib 0x18d7933b JNI_CreateJavaVM_Impl + 54155
6 libSystem.B.dylib 0x94e64a19 _pthread_start + 345
7 libSystem.B.dylib 0x94e6489e thread_start + 34

Thread 12: Java: CompilerThread0
0 libSystem.B.dylib 0x94e372fa mach_msg_trap + 10
1 libSystem.B.dylib 0x94e37a67 mach_msg + 68
2 libclient.dylib 0x18d79f23 JNI_CreateJavaVM_Impl + 57203
3 libclient.dylib 0x18d79dab JNI_CreateJavaVM_Impl + 56827
4 libclient.dylib 0x18d79928 JNI_CreateJavaVM_Impl + 55672
5 libclient.dylib 0x18d794a9 JNI_CreateJavaVM_Impl + 54521
6 libclient.dylib 0x18e3aec2 JVM_IsPrimitiveClass + 15362
7 libclient.dylib 0x18e3ac9b JVM_IsPrimitiveClass + 14811
8 libclient.dylib 0x18e21d74 JVM_InternString + 1188
9 libclient.dylib 0x18e2180f JVM_StartThread + 2175
10 libclient.dylib 0x18d7933b JNI_CreateJavaVM_Impl + 54155
11 libSystem.B.dylib 0x94e64a19 _pthread_start + 345
12 libSystem.B.dylib 0x94e6489e thread_start + 34

Thread 13: Java: Low Memory Detector
0 libSystem.B.dylib 0x94e372fa mach_msg_trap + 10
1 libSystem.B.dylib 0x94e37a67 mach_msg + 68
2 libclient.dylib 0x18d79f23 JNI_CreateJavaVM_Impl + 57203
3 libclient.dylib 0x18d79dab JNI_CreateJavaVM_Impl + 56827
4 libclient.dylib 0x18d79928 JNI_CreateJavaVM_Impl + 55672
5 libclient.dylib 0x18d79588 JNI_CreateJavaVM_Impl + 54744
6 libclient.dylib 0x18e3ee32 JVM_IsPrimitiveClass + 31602
7 libclient.dylib 0x18e21d74 JVM_InternString + 1188
8 libclient.dylib 0x18e2180f JVM_StartThread + 2175
9 libclient.dylib 0x18d7933b JNI_CreateJavaVM_Impl + 54155
10 libSystem.B.dylib 0x94e64a19 _pthread_start + 345
11 libSystem.B.dylib 0x94e6489e thread_start + 34

Thread 14: Java: VM Periodic Task Thread
0 libSystem.B.dylib 0x94e372fa mach_msg_trap + 10
1 libSystem.B.dylib 0x94e37a67 mach_msg + 68
2 libclient.dylib 0x18d7a037 JNI_CreateJavaVM_Impl + 57479
3 libclient.dylib 0x18e4010d JVM_IsPrimitiveClass + 36429
4 libclient.dylib 0x18e3fcb3 JVM_IsPrimitiveClass + 35315
5 libclient.dylib 0x18d7933b JNI_CreateJavaVM_Impl + 54155
6 libSystem.B.dylib 0x94e64a19 _pthread_start + 345
7 libSystem.B.dylib 0x94e6489e thread_start + 34

Thread 15:
0 libSystem.B.dylib 0x94e56286 select$DARWIN_EXTSN + 10
1 com.apple.CoreFoundation 0x98b1e82d __CFSocketManager + 1085
2 libSystem.B.dylib 0x94e64a19 _pthread_start + 345
3 libSystem.B.dylib 0x94e6489e thread_start + 34

Thread 16:
0 libSystem.B.dylib 0x94e372fa mach_msg_trap + 10
1 libSystem.B.dylib 0x94e37a67 mach_msg + 68
2 libclient.dylib 0x18d79f23 JNI_CreateJavaVM_Impl + 57203
3 libclient.dylib 0x18d79dab JNI_CreateJavaVM_Impl + 56827
4 libclient.dylib 0x18d79928 JNI_CreateJavaVM_Impl + 55672
5 libclient.dylib 0x18d794a9 JNI_CreateJavaVM_Impl + 54521
6 libclient.dylib 0x18e7546f JVM_EnableCompiler + 10991
7 libclient.dylib 0x18fdbebb pss + 234635
8 libclient.dylib 0x18e9ad04 JVM_GC + 468
9 libclient.dylib 0x18e9abf7 JVM_GC + 199
10 libjava.jnilib 0x193080ab Java_java_lang_Runtime_gc + 11
11 ??? 0x1a80b839 0 + 444643385
12 ??? 0x1a803db1 0 + 444612017
13 ??? 0x1a8012d3 0 + 444601043
14 libclient.dylib 0x18e107d0 JVM_Lseek + 149024
15 libclient.dylib 0x18e10576 JVM_Lseek + 148422
16 libclient.dylib 0x18e10546 JVM_Lseek + 148374
17 libclient.dylib 0x18e26230 JVM_MonitorWait + 15088
18 libclient.dylib 0x190064da pss + 408234
19 javabridge.so 0x18d5a92a initjavabridge + 74202
20 libpython2.5.dylib 0x00409dac PyObject_Call + 45
21 libpython2.5.dylib 0x004936e1 PyEval_EvalFrameEx + 14836
22 libpython2.5.dylib 0x0049671d PyEval_EvalCodeEx + 1819
23 libpython2.5.dylib 0x00493d9e PyEval_EvalFrameEx + 16561
24 libpython2.5.dylib 0x0049671d PyEval_EvalCodeEx + 1819
25 libpython2.5.dylib 0x00493d9e PyEval_EvalFrameEx + 16561
26 libpython2.5.dylib 0x00495b86 PyEval_EvalFrameEx + 24217
27 libpython2.5.dylib 0x00495b86 PyEval_EvalFrameEx + 24217
28 libpython2.5.dylib 0x0049671d PyEval_EvalCodeEx + 1819
29 libpython2.5.dylib 0x00493d9e PyEval_EvalFrameEx + 16561
30 libpython2.5.dylib 0x00495b86 PyEval_EvalFrameEx + 24217
31 libpython2.5.dylib 0x0049671d PyEval_EvalCodeEx + 1819
32 libpython2.5.dylib 0x0042b103 PyFunction_SetClosure + 1919
33 libpython2.5.dylib 0x00409dac PyObject_Call + 45
34 libpython2.5.dylib 0x00411aa7 PyMethod_New + 2432
35 libpython2.5.dylib 0x00409dac PyObject_Call + 45
36 libpython2.5.dylib 0x0048ee63 PyEval_CallObjectWithKeywords + 112
37 libpython2.5.dylib 0x004c9c73 _PyObject_GC_Del + 1845
38 libSystem.B.dylib 0x94e64a19 _pthread_start + 345
39 libSystem.B.dylib 0x94e6489e thread_start + 34

Thread 0 crashed with X86 Thread State (32-bit):
eax: 0x17e122c1 ebx: 0x98b21e51 ecx: 0x66e28ba0 edx: 0x00000020
edi: 0x1a09a510 esi: 0x66c8af6e ebp: 0xbfffcc48 esp: 0xbfffcc1c
ss: 0x0000001f efl: 0x00010246 eip: 0x1485100f cs: 0x00000017
ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037
cr2: 0x17e122c1

Binary Images:
0x1000 - 0x8ffd +org.pythonmac.unspecified.CellProfiler2.0 Revision: 9719 (Revision: 9719 ) <145CD1A7-E1D4-2ADD-8434-3ECFA3C34F3F> /Applications/CellProfiler2.0.app/Contents/MacOS/CellProfiler2.0
0xc8000 - 0xd9ffd +zlib.so ??? (???) /Applications/CellProfiler2.0.app/Contents/Resources/lib/python2.5/lib-dynload/zlib.so
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Model: MacBook6,1, BootROM MB61.00C8.B00, 2 processors, Intel Core 2 Duo, 2.26 GHz, 2 GB, SMC 1.51f53
Graphics: NVIDIA GeForce 9400M, NVIDIA GeForce 9400M, PCI, 256 MB
Memory Module: global_name
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x93), Broadcom BCM43xx 1.0 (5.10.131.14.7)
Bluetooth: Version 2.3.1f4, 2 service, 2 devices, 1 incoming serial ports
Network Service: AirPort, AirPort, en1
Serial ATA Device: Hitachi HTS545025B9SA02, 232.89 GB
Serial ATA Device: MATSHITADVD-R UJ-898
USB Device: Built-in iSight, 0x05ac (Apple Inc.), 0x8507, 0x24400000
USB Device: BRCM2070 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0x06100000
USB Device: Bluetooth Module, 0x05ac (Apple Inc.), 0x8218, 0x06130000
USB Device: Apple Internal Keyboard / Trackpad, 0x05ac (Apple Inc.), 0x0237, 0x04600000

Hello Linda,

I’ll try to reproduce this here. Could you post your pipeline and a few test images (a .zip file is fine)?

Thanks.

Thanks a lot! You’ll find the pipeline and images attached.
However, the problem is pipeline unspecific.

Thanks a lot for the help.
WT_2.tif.zip (2.05 MB)
WT_1.tif.zip (1.95 MB)
WT-PIPE-2.cp (7.17 KB)

I was able to reproduce the crash (though it’s a little different for me).

As a workaround, could you try changing the SaveImages module to write .PNG instead of .TIF? That avoids the crash on my system.

Thanks,
Ray

I found a fix, which will be in the next release.

If you want to be able to write 16-bit tiffs before that release, you can make this change to CellProfiler2.0.app/Contents/Resources/lib/python2.5/bioformats/init.py

After this line at the end of the file:

jutil.start_vm(__args)

Add:

jutil.attach() jutil.static_call("java/lang/System", "setProperty", '(Ljava/lang/String;Ljava/lang/String;)Ljava/lang/String;', "java.awt.headless", "TRUE") print "started headless",jutil.to_string(jutil.static_call("java/lang/System", "getProperty", '(Ljava/lang/String;)Ljava/lang/String;', "java.awt.headless")) jutil.detach()

The print statement is just for debugging.

If you’re comfortable making that change, I’m curious if it fixes the crash for you as well (it did for me).

Hey,

Thanks a lot for the help. In fact, I don’t even need the image to be saved as Tiff so I’m just fine with the png workaround for now.
It actually makes the pipeline faster!

Linda

For future reference (mostly for people encountering this thread through google), AWT calls should not be made in the main thread (even if Java is started in a second thread) on Mac. We’ll add a fix in the next release.