Manual Track in imageJ-TrackMate. I am using ImageJ on mac and when I select bands, the first one detected correctly, when I click cmd 2 (= ctr 2 on windows system) to detect the second band. Double-click on “ImageJ” (File Type = Application) Expand all contents. Shortly after, an expanded version of the “Fiji.app” folder. STARTING WITH FIJI. FOR MAC: Click on FIJI the application (which should be in your applications folder by now) FOR PC: Look for “Image J-win64” (file type: application) in your “Fiji.app” folder.
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
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Manual Tracking Imagej Macro
Manual Tracking Imagej Machine
Author: | Jesper Søndergaard Pedersen (jsp@phage.dk) |
History: | 2008/10/29: First version based on MTrack2, adding automatic counting of body-bends based on changes in angular speeds. Adding a speed histogram facility. Changed input value names to allow wrMTrck to be called from macros. 2008/11/29: Added body bend estimation based on aspect-ratio of animals 2009/03/22: Added maxSizeChange parameter to break tracks if objects change size. Measures Perimeter of object useful to estimate animal length = perimeter/2. Reports object speed in terms of body-lengths per seconds (BLPS) 2009/04/08: Machine independent textfile output by chaninging hard-coded 'n' to dos.newLine(). Changed maxAreaChange to a percentage instead of pixel value 2009/07/07: Added summarize feature. Added body-bend count display on showPositions movie. Added ability to override FPS. Now works with scale calibrated images. 2010/02/01: Corrected spelling mistake in input parameter “minTrackLength”(was “minTrackLenght”) - this may affect scripts using wrMTrck. 2010/04/11: Corrected names in some input fields on the dialog 2010/07/06: Added plotBendTrack option to allow output of thrashing quantification plots for trouble-shooting or quality control purposes. 2010/10/04: Now works on both binary and thresholded movies. Posibility to enable on the fly deflickering and simple background subtraction based on RB15 on first frame. This means that wrMTrck can now track animals in raw movies and virtual stacks. Hitting the ESC key aborts analysis. 2011/06/17: Added input field to allow adjustment of label font size 2011/06/22: Output of body-bend histogram (number of frames between half-bends) per animal only if bendDetect = 3 2011/10/31: Corrected undocumented raw data output with rawData =6 With rawData <0 headers are suppressed. (Konstantine Palanski) Summary repors frames with maximum and minimum number of objects and the frame with maximum number of tracked objects |
Requires: | ImageJ 1.34m or later |
Source: | wrMTrck_.java |
Installation: | Download wrmtrck.zip and unzip all files to the ..ImageJplugins folder and restart ImageJ. Note: Movie files can be very large and require a lot of memory (2GB+ RAM recommended) - see this page for information about how to increase memory available for ImageJ. Or even better use Fiji that automatically adjusts settings to give maximum memory |
Description: | wrMTrck plugin is based on Mtrack2 by Nico Stuurman, which is based on MultiTracker by Jeffrey Kuhn, which is based on Object_trackerby Wayne Rasband. wrMTrck will identify the objects in each frame, and then determine which objects in successive frames are closest together. If theses are within a user-defined distance (the maximum velocity of the objects) and have similar area (maxAreaChange) they are assembled into tracks. When multiple objects are within the distance determined by the maximum velocity, the closest object is selected and the object is flagged in the output. wrMTrck adds the following functionality to MTrack2:
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Citation | If you manange to publish work using this plugin feel free to cite the following paper : 'Investigating the spreading and toxicity of prion-like proteins using the metazoan model organism C. elegans.' by Nussbaum-Krammer CI, Neto MF, Brielmann RM, Pedersen JS, Morimoto RI |
See Also: | Object Tracker, Manual Tracking, MultitrackerCASA (Computer Assisted Sperm Analyzer), SpotTracker, MTrack2, ParticleTracker and MTrackJ plugins. |
Instructions | Instructions for usage is available in wrMTrck.pdf and wrMTrck_batch.pdf |
Demo files | Demo files are available here: N2.aviQ35.aviG85R.avi - movies are 30s long recorded at 60 pixel/mm scaling of animals at day 3 of adulthood grown at 25°C. Note: Movies of a variety of dfferent file formats can be loaded into ImageJ using LOCI Bio-Formats plugin or the quicktime plugin for ImageJ to load quicktime movies. |
Video tutorial | The video tutorial below demonstrates how to use ImageJ functions to enhance a raw movie and use wrMTrck to measure thrashing rates for swimming C. elegans The second video tutorial demonstrates how to use the wrMTrck_Batch to completely automate all of the steps involved in the movie enhancement and tracking enabling automated analysis of several movies in a folder. A video showcasing the some of the improvements included in build 101004, notably processing of thresholded images and virtual stacks |
Previous versions | In case new bugs were accidentally included in the most recent build here are some of the older builds: |
Manual Tracking Imagej
|Plugins | Home |