Thumbnail preview crashes Cell Profiler Analyst

Hi everyone,

since the latest CPA has been released, I finally decided to jump-in CP/CPA tutorials.

I’ve been following quite succesfully the TranslocationTutorial_v2.pdf (FOXO1A Tutorial) until I found 2 maybe related steps; which totally crash CPA (3.0.0 on macos 10.15.7 Catalina).

The first part (Done with freshly Installed CP 4.1.3) went well (I guess) and I got the SQlite db with overlay.tiffs as expected.

While following the second part of the tutorial, CPA crashes always at two different steps without any warning or log.

Crash A: When I follow the tutorial and choose in Plate Viewer the thumbnail well Display. It crashed immediately.

Crash B: When I follow the tutorial / open the Classifier / Fetch 20 random cells and start sorting them.
CPA crashes quite randomly after sorting from 2 to 8 cells approx.

Here is the log if it could help

Logging level: INFO
[Properties]: Loading DefaultDB_MyExpt.properties
[Properties] INFO: Unrecognized field "series_id" in properties file
[Properties] INFO: Unrecognized field "group_id" in properties file
[Properties] INFO: Unrecognized field "timepoint_id" in properties file
[Properties] INFO (channels_per_image): No value(s) specified. CPA will assume 1 channel per image.
[Properties]: Using default image_buffer_size=1
[Properties]: Using default tile_buffer_size=1
[Properties]: Per-Object classes will be written to table "MyExpt_"
[Properties] WARNING (well_format): Field was not defined, using default format of "A01".
[MainThread] Connecting to the database...
[MainThread] SQLite file: /Users/goran/Desktop/TempCellprofiler/DefaultDB.db
Logging level: DEBUG

Do you have any hint what might be wrong?
Do you need anything else hrom my side what might help?

Thanks in advance

Goran

PS: Here’s the Crash log if it could help:

Process:               cpanalyst [33838]
Path:                  /Applications/CellProfiler-Analyst.app/Contents/MacOS/cpanalyst
Identifier:            org.cellprofiler.CellProfiler-Analyst
Version:               3.0.0 (3.0.0)
Code Type:             X86-64 (Native)
Parent Process:        ??? [1]
Responsible:           cpanalyst [33838]
User ID:               503

Date/Time:             2021-04-30 14:49:18.535 +0200
OS Version:            Mac OS X 10.15.7 (19H524)
Report Version:        12
Anonymous UUID:        C4170EE9-7010-5868-90CD-5F00B6EBD483

Sleep/Wake UUID:       F38F7846-52AD-4134-B484-20642C693C74

Time Awake Since Boot: 230000 seconds
Time Since Wake:       6300 seconds

System Integrity Protection: enabled

Crashed Thread:        0  Dispatch queue: com.apple.main-thread

Exception Type:        EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:       KERN_INVALID_ADDRESS at 0x0000206a20f5c2c0
Exception Note:        EXC_CORPSE_NOTIFY

Termination Signal:    Segmentation fault: 11
Termination Reason:    Namespace SIGNAL, Code 0xb
Terminating Process:   exc handler [33838]

VM Regions Near 0x206a20f5c2c0:
    CoreAnimation          00000001337b2000-0000000133a3e000 [ 2608K] rw-/rwx SM=PRV  
--> 
    MALLOC_NANO            0000600000000000-0000600008000000 [128.0M] rw-/rwx SM=PRV  

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   libobjc.A.dylib               	0x00007fff726ffcb8 objc_release + 24
1   com.apple.CoreFoundation      	0x00007fff398cbc2c __RELEASE_OBJECTS_IN_THE_SET__ + 132
2   com.apple.CoreFoundation      	0x00007fff398cbb63 -[__NSSetM dealloc] + 128
3   com.apple.AppKit              	0x00007fff36ecb00c -[_NSPasteboardTypeCache dealloc] + 35
4   libobjc.A.dylib               	0x00007fff7271b356 AutoreleasePoolPage::releaseUntil(objc_object**) + 134
5   libobjc.A.dylib               	0x00007fff727003fc objc_autoreleasePoolPop + 175
6   com.apple.CoreFoundation      	0x00007fff398ad359 _CFAutoreleasePoolPop + 22
7   com.apple.Foundation          	0x00007fff3bf7e6fe -[NSAutoreleasePool drain] + 126
8   com.apple.AppKit              	0x00007fff36b3e5f2 -[NSApplication run] + 758
9   libwx_osx_cocoau_core-3.1.5.0.0.dylib	0x000000012210c59f wxGUIEventLoop::OSXDoRun() + 207
10  libwx_baseu-3.1.5.0.0.dylib   	0x000000012291eb51 wxCFEventLoop::DoRun() + 49
11  libwx_baseu-3.1.5.0.0.dylib   	0x00000001228610ae wxEventLoopBase::Run() + 158
12  libwx_baseu-3.1.5.0.0.dylib   	0x000000012282d483 wxAppConsoleBase::MainLoop() + 99
13  _core.cpython-38-darwin.so    	0x000000012152e591 meth_wxPyApp_MainLoop(_object*, _object*) + 209
14  libpython3.8.dylib            	0x000000010c994830 cfunction_call_varargs + 224
15  libpython3.8.dylib            	0x000000010c993a07 _PyObject_MakeTpCall + 167
16  libpython3.8.dylib            	0x000000010cadcd1f _PyEval_EvalFrameDefault + 47999
17  libpython3.8.dylib            	0x000000010c994fbf _PyFunction_Vectorcall + 223
18  libpython3.8.dylib            	0x000000010cadcb2e _PyEval_EvalFrameDefault + 47502
19  libpython3.8.dylib            	0x000000010cacf47f _PyEval_EvalCodeWithName + 495
20  libpython3.8.dylib            	0x000000010cacf280 PyEval_EvalCode + 48
21  org.cellprofiler.CellProfiler-Analyst	0x000000010bcd619e 0x10bcd3000 + 12702
22  org.cellprofiler.CellProfiler-Analyst	0x000000010bcd6609 0x10bcd3000 + 13833
23  org.cellprofiler.CellProfiler-Analyst	0x000000010bcd6861 0x10bcd3000 + 14433
24  org.cellprofiler.CellProfiler-Analyst	0x000000010bcd47e4 0x10bcd3000 + 6116

Thread 1:: com.apple.NSEventThread
0   libsystem_kernel.dylib        	0x00007fff739ebdfa mach_msg_trap + 10
1   libsystem_kernel.dylib        	0x00007fff739ec170 mach_msg + 60
2   com.apple.CoreFoundation      	0x00007fff398efa27 __CFRunLoopServiceMachPort + 247
3   com.apple.CoreFoundation      	0x00007fff398ee4e1 __CFRunLoopRun + 1329
4   com.apple.CoreFoundation      	0x00007fff398ed953 CFRunLoopRunSpecific + 466
5   com.apple.AppKit              	0x00007fff36cef954 _NSEventThread + 132
6   libsystem_pthread.dylib       	0x00007fff73ab3109 _pthread_start + 148
7   libsystem_pthread.dylib       	0x00007fff73aaeb8b thread_start + 15

Thread 2:
0   libsystem_kernel.dylib        	0x00007fff739ee882 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff73ab3425 _pthread_cond_wait + 698
2   com.apple.GeForceMTLDriver    	0x00007fff35047cbb 0x7fff34edb000 + 1494203
3   libsystem_pthread.dylib       	0x00007fff73ab3109 _pthread_start + 148
4   libsystem_pthread.dylib       	0x00007fff73aaeb8b thread_start + 15

Thread 3:
0   libsystem_kernel.dylib        	0x00007fff739ee882 __psynch_cvwait + 10
1   libsystem_pthread.dylib       	0x00007fff73ab3425 _pthread_cond_wait + 698
2   libpython3.8.dylib            	0x000000010cb6249b PyThread_acquire_lock_timed + 171
3   libpython3.8.dylib            	0x000000010cbd801d acquire_timed + 301
4   libpython3.8.dylib            	0x000000010cbd830c lock_PyThread_acquire_lock + 44
5   libpython3.8.dylib            	0x000000010c9a3493 method_vectorcall_VARARGS_KEYWORDS + 387
6   libpython3.8.dylib            	0x000000010cadcb2e _PyEval_EvalFrameDefault + 47502
7   libpython3.8.dylib            	0x000000010cacf47f _PyEval_EvalCodeWithName + 495
8   libpython3.8.dylib            	0x000000010c995071 _PyFunction_Vectorcall + 401
9   libpython3.8.dylib            	0x000000010cadcb2e _PyEval_EvalFrameDefault + 47502
10  libpython3.8.dylib            	0x000000010c994fbf _PyFunction_Vectorcall + 223
11  libpython3.8.dylib            	0x000000010cadcb2e _PyEval_EvalFrameDefault + 47502
12  libpython3.8.dylib            	0x000000010c994fbf _PyFunction_Vectorcall + 223
13  libpython3.8.dylib            	0x000000010cadcb2e _PyEval_EvalFrameDefault + 47502
14  libpython3.8.dylib            	0x000000010c994fbf _PyFunction_Vectorcall + 223
15  libpython3.8.dylib            	0x000000010c998d9e method_vectorcall + 494
16  libpython3.8.dylib            	0x000000010c9943cb PyVectorcall_Call + 107
17  libpython3.8.dylib            	0x000000010cbd75a4 t_bootstrap + 212
18  libpython3.8.dylib            	0x000000010cb62164 pythread_wrapper + 36
19  libsystem_pthread.dylib       	0x00007fff73ab3109 _pthread_start + 148
20  libsystem_pthread.dylib       	0x00007fff73aaeb8b thread_start + 15

Thread 4:
0   libsystem_pthread.dylib       	0x00007fff73aaeb68 start_wqthread + 0

Thread 5:
0   libsystem_pthread.dylib       	0x00007fff73aaeb68 start_wqthread + 0

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x0000206a20f5c2a0  rbx: 0x0000000000000002  rcx: 0x00007fff39b8b980  rdx: 0x0040000000000000
  rdi: 0x00006000006ec2a0  rsi: 0x0000000000000001  rbp: 0x00007ffee3f2b280  rsp: 0x00007ffee3f2b248
   r8: 0x0000000000000154   r9: 0x00000000000007fb  r10: 0x00007fff9121d628  r11: 0x00007fff398cbae3
  r12: 0x0000000000000001  r13: 0x00007fff911228d8  r14: 0x000060000089a900  r15: 0x0000000000000003
  rip: 0x00007fff726ffcb8  rfl: 0x0000000000010206  cr2: 0x0000206a20f5c2c0
  
Logical CPU:     0
Error Code:      0x00000004 (no mapping for user data read)
Trap Number:     14


Binary Images:
       0x10bcd3000 -        0x10bcddff7 +org.cellprofiler.CellProfiler-Analyst (3.0.0 - 3.0.0) <60F2963C-6766-3803-82E9-5322BB718ED7> /Applications/CellProfiler-Analyst.app/Contents/MacOS/cpanalyst
       0x10c967000 -        0x10cc8dfff +libpython3.8.dylib (0) <8DC9F760-7F1F-3C23-B0FE-47137B846E0A> /Applications/CellProfiler-Analyst.app/Contents/MacOS/libpython3.8.dylib
       0x10cdd6000 -        0x10cddffff +libintl.8.dylib (0) <FA921CC0-395B-3155-8259-EA61DE25C5D2> /Applications/CellProfiler-Analyst.app/Contents/MacOS/libintl.8.dylib
       0x10cf2b000 -        0x10cf31fff +_struct.cpython-38-darwin.so (0) <AD041118-CECD-36D1-A530-60715002F191> /Applications/CellProfiler-Analyst.app/Contents/MacOS/lib-dynload/_struct.cpython-38-darwin.so
       0x10cf3d000 -        0x10cf42fff +zlib.cpython-38-darwin.so (0) <8CC1097C-C689-34AD-8C32-C00981A1317F> /Applications/CellProfiler-Analyst.app/Contents/MacOS/lib-dynload/zlib.cpython-38-darwin.so
********too long 


Thanks for reporting this! We’ve found a fix for Crash A, currently working on Crash B. Hope to have both fixed for v3.0.1.

In the meantime, it might be worth trying to see if you can move items into the classification bins by using the keyboard shortcuts - select a tile with the arrow keys and use the number keys to move them to a class.

1 Like

Yes I can!
It works perfectly as soon as I don’t drag/drop cells

Just released v3.0.1, which should fix this. Thanks for reporting!

I should thank YOU, for the superfast bugfix.
Everything works now :+1:
That will allow me to continue nicely done tutorial(s). :grinning_face_with_smiling_eyes:

1 Like