trackmate
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Hello,
I am currently embarking on a project that requires a lot of cell tracking and have started to investigate whether trackmate could aid me. My experiments involve tracking neuroblast lineages as they develop in the drosophila embryo. To track and visualise cells and their divisions I am using a pan histone GFP. As such there is a high population and density of cells that are marked. I was wondering if it was possible to use trackmate to follow just one cell and its progeny instead of everything? Also, is it possible to manually edit the output that trackmate provides if I do not agree with a decision that the software has made? Many thanks, Holly |
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Dear users, I have a "new" error in my python scripts since last update... I used to say (mac OS X 10.6.8 Fiji 1.48v Java 1.6.0065 64bits):
import os os.makedirs("/Users/leon/Desktop/temp/temp", mode=0777) And now it says : Traceback (most recent call last): File "<iostream>", line 4, in <module> File "/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/os.py", line 149, in makedirs File "/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py", line 171, in exists File "/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py", line 171, in exists java.lang.IncompatibleClassChangeError: Found class com.kenai.jffi.InvocationBuffer, but interface was expected at com.kenai.jaffl.provider.jffi.AsmRuntime.marshal(AsmRuntime.java:167) at org.python.posix.LibC$jaffl$0.stat$raw(Unknown Source) at org.python.posix.LibC$jaffl$0.stat(Unknown Source) at org.python.posix.BaseNativePOSIX.stat(BaseNativePOSIX.java:200) at org.python.posix.LazyPOSIX.stat(LazyPOSIX.java:207) at org.python.modules.posix.PosixModule$StatFunction.__call__(PosixModule.java:966) at posixpath$py.exists$15(/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py:174) at posixpath$py.call_function(/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py) at org.python.core.PyTableCode.call(PyTableCode.java:165) at org.python.core.PyBaseCode.call(PyBaseCode.java:134) at org.python.core.PyFunction.__call__(PyFunction.java:317) at os$py.makedirs$2(/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/os.py:158) at os$py.call_function(/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/os.py) at org.python.core.PyTableCode.call(PyTableCode.java:165) at org.python.core.PyBaseCode.call(PyBaseCode.java:301) at org.python.core.PyFunction.function___call__(PyFunction.java:376) at org.python.core.PyFunction.__call__(PyFunction.java:371) at org.python.pycode._pyx9.f$0(<iostream>:4) at org.python.pycode._pyx9.call_function(<iostream>) at org.python.core.PyTableCode.call(PyTableCode.java:165) at org.python.core.PyCode.call(PyCode.java:18) at org.python.core.Py.runCode(Py.java:1261) at org.python.util.PythonInterpreter.execfile(PythonInterpreter.java:235) at org.python.util.PythonInterpreter.execfile(PythonInterpreter.java:230) at Jython.Refresh_Jython_Scripts.runScript(Refresh_Jython_Scripts.java:73) at common.RefreshScripts.runScript(RefreshScripts.java:328) at fiji.scripting.TextEditor$Tab$6.execute(TextEditor.java:1225) at fiji.scripting.TextEditor$Executer$1.run(TextEditor.java:1785) java.lang.IncompatibleClassChangeError: java.lang.IncompatibleClassChangeError: Found class com.kenai.jffi.InvocationBuffer, but interface was expected thank you for any help... ! All the best, Leon -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Leon
I got the same thing. I believe it is because of a conflict between components packaged with both jython and jruby. jruby was updated recently. When I deleted ruby-complete-1.7.11.jar from the jars directory the jython scripts started working again. This is a hack though because then jruby doesn't work. Brian On Tue, May 6, 2014 at 8:07 AM, Leon Espinosa <[hidden email]>wrote: > Dear users, I have a "new" error in my python scripts since last update... > I used to say (mac OS X 10.6.8 Fiji 1.48v Java 1.6.0065 64bits): > > > import os > os.makedirs("/Users/leon/Desktop/temp/temp", mode=0777) > > > And now it says : > > > Traceback (most recent call last): > File "<iostream>", line 4, in <module> > File "/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/os.py", line 149, > in makedirs > File "/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py", > line 171, in exists > File "/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py", > line 171, in exists > java.lang.IncompatibleClassChangeError: Found class > com.kenai.jffi.InvocationBuffer, but interface was expected > at > com.kenai.jaffl.provider.jffi.AsmRuntime.marshal(AsmRuntime.java:167) > at org.python.posix.LibC$jaffl$0.stat$raw(Unknown Source) > at org.python.posix.LibC$jaffl$0.stat(Unknown Source) > at org.python.posix.BaseNativePOSIX.stat(BaseNativePOSIX.java:200) > at org.python.posix.LazyPOSIX.stat(LazyPOSIX.java:207) > at > org.python.modules.posix.PosixModule$StatFunction.__call__(PosixModule.java:966) > at > posixpath$py.exists$15(/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py:174) > at > posixpath$py.call_function(/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py) > at org.python.core.PyTableCode.call(PyTableCode.java:165) > at org.python.core.PyBaseCode.call(PyBaseCode.java:134) > at org.python.core.PyFunction.__call__(PyFunction.java:317) > at > os$py.makedirs$2(/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/os.py:158) > at > os$py.call_function(/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/os.py) > at org.python.core.PyTableCode.call(PyTableCode.java:165) > at org.python.core.PyBaseCode.call(PyBaseCode.java:301) > at > org.python.core.PyFunction.function___call__(PyFunction.java:376) > at org.python.core.PyFunction.__call__(PyFunction.java:371) > at org.python.pycode._pyx9.f$0(<iostream>:4) > at org.python.pycode._pyx9.call_function(<iostream>) > at org.python.core.PyTableCode.call(PyTableCode.java:165) > at org.python.core.PyCode.call(PyCode.java:18) > at org.python.core.Py.runCode(Py.java:1261) > at > org.python.util.PythonInterpreter.execfile(PythonInterpreter.java:235) > at > org.python.util.PythonInterpreter.execfile(PythonInterpreter.java:230) > at > Jython.Refresh_Jython_Scripts.runScript(Refresh_Jython_Scripts.java:73) > at common.RefreshScripts.runScript(RefreshScripts.java:328) > at fiji.scripting.TextEditor$Tab$6.execute(TextEditor.java:1225) > at fiji.scripting.TextEditor$Executer$1.run(TextEditor.java:1785) > > java.lang.IncompatibleClassChangeError: > java.lang.IncompatibleClassChangeError: Found class > com.kenai.jffi.InvocationBuffer, but interface was expected > > > thank you for any help... ! > > All the best, Leon > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: new error in a python script
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Thank you Brian !!
You are right without ruby-complete-1.7.11.jar it works again... Now my problem is that there are 20 people that use my scripts in the lab... it will be difficult to remove de file for all (humm... even find it !) and to delete it again if updates put it back... Leon Le 6 mai 2014 à 13:56, Brian Northan a écrit : > Hi Leon > > I got the same thing. I believe it is because of a conflict between > components packaged with both jython and jruby. > > jruby was updated recently. When I deleted ruby-complete-1.7.11.jar from > the jars directory the jython scripts started working again. This is a > hack though because then jruby doesn't work. > > Brian > > > On Tue, May 6, 2014 at 8:07 AM, Leon Espinosa <[hidden email]>wrote: > >> Dear users, I have a "new" error in my python scripts since last update... >> I used to say (mac OS X 10.6.8 Fiji 1.48v Java 1.6.0065 64bits): >> >> >> import os >> os.makedirs("/Users/leon/Desktop/temp/temp", mode=0777) >> >> >> And now it says : >> >> >> Traceback (most recent call last): >> File "<iostream>", line 4, in <module> >> File "/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/os.py", line 149, >> in makedirs >> File "/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py", >> line 171, in exists >> File "/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py", >> line 171, in exists >> java.lang.IncompatibleClassChangeError: Found class >> com.kenai.jffi.InvocationBuffer, but interface was expected >> at >> com.kenai.jaffl.provider.jffi.AsmRuntime.marshal(AsmRuntime.java:167) >> at org.python.posix.LibC$jaffl$0.stat$raw(Unknown Source) >> at org.python.posix.LibC$jaffl$0.stat(Unknown Source) >> at org.python.posix.BaseNativePOSIX.stat(BaseNativePOSIX.java:200) >> at org.python.posix.LazyPOSIX.stat(LazyPOSIX.java:207) >> at >> org.python.modules.posix.PosixModule$StatFunction.__call__(PosixModule.java:966) >> at >> posixpath$py.exists$15(/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py:174) >> at >> posixpath$py.call_function(/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py) >> at org.python.core.PyTableCode.call(PyTableCode.java:165) >> at org.python.core.PyBaseCode.call(PyBaseCode.java:134) >> at org.python.core.PyFunction.__call__(PyFunction.java:317) >> at >> os$py.makedirs$2(/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/os.py:158) >> at >> os$py.call_function(/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/os.py) >> at org.python.core.PyTableCode.call(PyTableCode.java:165) >> at org.python.core.PyBaseCode.call(PyBaseCode.java:301) >> at >> org.python.core.PyFunction.function___call__(PyFunction.java:376) >> at org.python.core.PyFunction.__call__(PyFunction.java:371) >> at org.python.pycode._pyx9.f$0(<iostream>:4) >> at org.python.pycode._pyx9.call_function(<iostream>) >> at org.python.core.PyTableCode.call(PyTableCode.java:165) >> at org.python.core.PyCode.call(PyCode.java:18) >> at org.python.core.Py.runCode(Py.java:1261) >> at >> org.python.util.PythonInterpreter.execfile(PythonInterpreter.java:235) >> at >> org.python.util.PythonInterpreter.execfile(PythonInterpreter.java:230) >> at >> Jython.Refresh_Jython_Scripts.runScript(Refresh_Jython_Scripts.java:73) >> at common.RefreshScripts.runScript(RefreshScripts.java:328) >> at fiji.scripting.TextEditor$Tab$6.execute(TextEditor.java:1225) >> at fiji.scripting.TextEditor$Executer$1.run(TextEditor.java:1785) >> >> java.lang.IncompatibleClassChangeError: >> java.lang.IncompatibleClassChangeError: Found class >> com.kenai.jffi.InvocationBuffer, but interface was expected >> >> >> thank you for any help... ! >> >> All the best, Leon >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Holly
Hi Holly
Good luck on your project! TrackMate can help you, however in a limited fashion. When there are many cells labeled densely packed together, the tracking algorithm can get confused quickly. Particularly if the cells move and/or divide. Fortunately for us your goal seems to be more modest as you want to follow a sparse number of cells in your data. TrackMate offers semi-automated framework where you can manually annotate a movie and follow a cell lineage. There is a tutorial for this here: http://fiji.sc/Manual_tracking_with_TrackMate Best jy -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Leon Espinosa-3
Hi Leon,
> You are right without ruby-complete-1.7.11.jar it works again... Now > my problem is that there are 20 people that use my scripts in the > lab... it will be difficult to remove de file for all (humm... even > find it !) and to delete it again if updates put it back... Sorry for the problems. For what it's worth, this is a known issue we plan on fixing: https://github.com/fiji/fiji/issues/83 But it may be a few weeks until we can fully resolve the problem. Regards, Curtis On Tue, May 6, 2014 at 7:37 AM, Leon Espinosa <[hidden email]>wrote: > Thank you Brian !! > You are right without ruby-complete-1.7.11.jar it works again... Now my > problem is that there are 20 people that use my scripts in the lab... it > will be difficult to remove de file for all (humm... even find it !) and to > delete it again if updates put it back... > > Leon > > > > Le 6 mai 2014 à 13:56, Brian Northan a écrit : > > > Hi Leon > > > > I got the same thing. I believe it is because of a conflict between > > components packaged with both jython and jruby. > > > > jruby was updated recently. When I deleted ruby-complete-1.7.11.jar > from > > the jars directory the jython scripts started working again. This is a > > hack though because then jruby doesn't work. > > > > Brian > > > > > > On Tue, May 6, 2014 at 8:07 AM, Leon Espinosa < > [hidden email]>wrote: > > > >> Dear users, I have a "new" error in my python scripts since last > update... > >> I used to say (mac OS X 10.6.8 Fiji 1.48v Java 1.6.0065 64bits): > >> > >> > >> import os > >> os.makedirs("/Users/leon/Desktop/temp/temp", mode=0777) > >> > >> > >> And now it says : > >> > >> > >> Traceback (most recent call last): > >> File "<iostream>", line 4, in <module> > >> File "/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/os.py", line > 149, > >> in makedirs > >> File "/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py", > >> line 171, in exists > >> File "/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py", > >> line 171, in exists > >> java.lang.IncompatibleClassChangeError: Found class > >> com.kenai.jffi.InvocationBuffer, but interface was expected > >> at > >> com.kenai.jaffl.provider.jffi.AsmRuntime.marshal(AsmRuntime.java:167) > >> at org.python.posix.LibC$jaffl$0.stat$raw(Unknown Source) > >> at org.python.posix.LibC$jaffl$0.stat(Unknown Source) > >> at > org.python.posix.BaseNativePOSIX.stat(BaseNativePOSIX.java:200) > >> at org.python.posix.LazyPOSIX.stat(LazyPOSIX.java:207) > >> at > >> > org.python.modules.posix.PosixModule$StatFunction.__call__(PosixModule.java:966) > >> at > >> > posixpath$py.exists$15(/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py:174) > >> at > >> > posixpath$py.call_function(/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py) > >> at org.python.core.PyTableCode.call(PyTableCode.java:165) > >> at org.python.core.PyBaseCode.call(PyBaseCode.java:134) > >> at org.python.core.PyFunction.__call__(PyFunction.java:317) > >> at > >> > os$py.makedirs$2(/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/os.py:158) > >> at > >> > os$py.call_function(/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/os.py) > >> at org.python.core.PyTableCode.call(PyTableCode.java:165) > >> at org.python.core.PyBaseCode.call(PyBaseCode.java:301) > >> at > >> org.python.core.PyFunction.function___call__(PyFunction.java:376) > >> at org.python.core.PyFunction.__call__(PyFunction.java:371) > >> at org.python.pycode._pyx9.f$0(<iostream>:4) > >> at org.python.pycode._pyx9.call_function(<iostream>) > >> at org.python.core.PyTableCode.call(PyTableCode.java:165) > >> at org.python.core.PyCode.call(PyCode.java:18) > >> at org.python.core.Py.runCode(Py.java:1261) > >> at > >> org.python.util.PythonInterpreter.execfile(PythonInterpreter.java:235) > >> at > >> org.python.util.PythonInterpreter.execfile(PythonInterpreter.java:230) > >> at > >> Jython.Refresh_Jython_Scripts.runScript(Refresh_Jython_Scripts.java:73) > >> at common.RefreshScripts.runScript(RefreshScripts.java:328) > >> at fiji.scripting.TextEditor$Tab$6.execute(TextEditor.java:1225) > >> at fiji.scripting.TextEditor$Executer$1.run(TextEditor.java:1785) > >> > >> java.lang.IncompatibleClassChangeError: > >> java.lang.IncompatibleClassChangeError: Found class > >> com.kenai.jffi.InvocationBuffer, but interface was expected > >> > >> > >> thank you for any help... ! > >> > >> All the best, Leon > >> > >> -- > >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html > >> > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: new error in a python script
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Dear Curtis, thank you for this information. If it is a known issue it is perfect for me.
And also thank you for all the work on Fiji/ImageJ !! All the best, Leon Le 7 mai 2014 à 10:35, Curtis Rueden a écrit : > Hi Leon, > >> You are right without ruby-complete-1.7.11.jar it works again... Now >> my problem is that there are 20 people that use my scripts in the >> lab... it will be difficult to remove de file for all (humm... even >> find it !) and to delete it again if updates put it back... > > Sorry for the problems. For what it's worth, this is a known issue we plan > on fixing: > https://github.com/fiji/fiji/issues/83 > > But it may be a few weeks until we can fully resolve the problem. > > Regards, > Curtis > > > On Tue, May 6, 2014 at 7:37 AM, Leon Espinosa <[hidden email]>wrote: > >> Thank you Brian !! >> You are right without ruby-complete-1.7.11.jar it works again... Now my >> problem is that there are 20 people that use my scripts in the lab... it >> will be difficult to remove de file for all (humm... even find it !) and to >> delete it again if updates put it back... >> >> Leon >> >> >> >> Le 6 mai 2014 à 13:56, Brian Northan a écrit : >> >>> Hi Leon >>> >>> I got the same thing. I believe it is because of a conflict between >>> components packaged with both jython and jruby. >>> >>> jruby was updated recently. When I deleted ruby-complete-1.7.11.jar >> from >>> the jars directory the jython scripts started working again. This is a >>> hack though because then jruby doesn't work. >>> >>> Brian >>> >>> >>> On Tue, May 6, 2014 at 8:07 AM, Leon Espinosa < >> [hidden email]>wrote: >>> >>>> Dear users, I have a "new" error in my python scripts since last >> update... >>>> I used to say (mac OS X 10.6.8 Fiji 1.48v Java 1.6.0065 64bits): >>>> >>>> >>>> import os >>>> os.makedirs("/Users/leon/Desktop/temp/temp", mode=0777) >>>> >>>> >>>> And now it says : >>>> >>>> >>>> Traceback (most recent call last): >>>> File "<iostream>", line 4, in <module> >>>> File "/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/os.py", line >> 149, >>>> in makedirs >>>> File "/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py", >>>> line 171, in exists >>>> File "/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py", >>>> line 171, in exists >>>> java.lang.IncompatibleClassChangeError: Found class >>>> com.kenai.jffi.InvocationBuffer, but interface was expected >>>> at >>>> com.kenai.jaffl.provider.jffi.AsmRuntime.marshal(AsmRuntime.java:167) >>>> at org.python.posix.LibC$jaffl$0.stat$raw(Unknown Source) >>>> at org.python.posix.LibC$jaffl$0.stat(Unknown Source) >>>> at >> org.python.posix.BaseNativePOSIX.stat(BaseNativePOSIX.java:200) >>>> at org.python.posix.LazyPOSIX.stat(LazyPOSIX.java:207) >>>> at >>>> >> org.python.modules.posix.PosixModule$StatFunction.__call__(PosixModule.java:966) >>>> at >>>> >> posixpath$py.exists$15(/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py:174) >>>> at >>>> >> posixpath$py.call_function(/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/posixpath.py) >>>> at org.python.core.PyTableCode.call(PyTableCode.java:165) >>>> at org.python.core.PyBaseCode.call(PyBaseCode.java:134) >>>> at org.python.core.PyFunction.__call__(PyFunction.java:317) >>>> at >>>> >> os$py.makedirs$2(/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/os.py:158) >>>> at >>>> >> os$py.call_function(/Applications/Fiji.app/jars/jython-2.5.2.jar/Lib/os.py) >>>> at org.python.core.PyTableCode.call(PyTableCode.java:165) >>>> at org.python.core.PyBaseCode.call(PyBaseCode.java:301) >>>> at >>>> org.python.core.PyFunction.function___call__(PyFunction.java:376) >>>> at org.python.core.PyFunction.__call__(PyFunction.java:371) >>>> at org.python.pycode._pyx9.f$0(<iostream>:4) >>>> at org.python.pycode._pyx9.call_function(<iostream>) >>>> at org.python.core.PyTableCode.call(PyTableCode.java:165) >>>> at org.python.core.PyCode.call(PyCode.java:18) >>>> at org.python.core.Py.runCode(Py.java:1261) >>>> at >>>> org.python.util.PythonInterpreter.execfile(PythonInterpreter.java:235) >>>> at >>>> org.python.util.PythonInterpreter.execfile(PythonInterpreter.java:230) >>>> at >>>> Jython.Refresh_Jython_Scripts.runScript(Refresh_Jython_Scripts.java:73) >>>> at common.RefreshScripts.runScript(RefreshScripts.java:328) >>>> at fiji.scripting.TextEditor$Tab$6.execute(TextEditor.java:1225) >>>> at fiji.scripting.TextEditor$Executer$1.run(TextEditor.java:1785) >>>> >>>> java.lang.IncompatibleClassChangeError: >>>> java.lang.IncompatibleClassChangeError: Found class >>>> com.kenai.jffi.InvocationBuffer, but interface was expected >>>> >>>> >>>> thank you for any help... ! >>>> >>>> All the best, Leon >>>> >>>> -- >>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >>>> >>> >>> -- >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Jean-Yves Tinevez
Hi Jean-Tves,
Thanks very much for your help. It seems this tool will be very useful for me. I was wondering if you know if it is possible to carry out manual tracking while simultaneously viewing orthogonal views? Many thanks, Holly
___________________ Dr. Holly Ironfield Landgraf Lab Department of Zoology Downing Street Cambridge CB2 3EJ On 7 May 2014, at 08:05, Jean-Yves Tinevez-3 [via ImageJ] wrote: Hi Holly |
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In reply to this post by Holly
Hi Holly.
No. The current displayer is only our plain Hyperstack view. Best jy -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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