hansenjn / ciliaq_preparator Goto Github PK
View Code? Open in Web Editor NEWAn ImageJ plugin to prepare images for analysis using CiliaQ.
License: GNU General Public License v3.0
An ImageJ plugin to prepare images for analysis using CiliaQ.
License: GNU General Public License v3.0
When running an image that is not saved, CiliaQ Preparator crashes with the error message:
java.lang.NullPointerException
at ciliaQ_Prep_jnh.CiliaQPrepMain.run(CiliaQPrepMain.java:273)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:750)
TODO:
Catch the error and output an interpretable message to the user explaining how the user can avoid this issue.
The segmentation based on CANNY3D is applied to the first channel, even when a different channel is selected for segmentation.
Hello Hansen,
Thank you for providing us this powerful plugin! After processing my 2D pictures with CANNY 3D through CiliaQ Preparator, I found that some cilia from the segmented channel showed a loss of pixels, but not all the cilia. It looks like the ciliaQ won't pick these missing pixels finally when we quantify the cilia intensity. Would you have any good suggestions? Thanks!
Recently errors occur when applying "HYSTERESIS threshold" or "CANNY3D" as the "Segmentation method", but only when the image was loaded through the multi-task manager processing option ( ).
For CANNY 3D, two error messages appear:
Message 1:
java.lang.NullPointerException
at ciliaQ_Prep_jnh.canny3d_thresholder.Processing.doProcessing(Processing.java:52)
at ciliaQ_Prep_jnh.CiliaQPrepMain.segmentUsingCanny3D(CiliaQPrepMain.java:1437)
at ciliaQ_Prep_jnh.CiliaQPrepMain.run(CiliaQPrepMain.java:567)
at ij.IJ.runUserPlugIn(IJ.java:244)
at ij.IJ.runPlugIn(IJ.java:210)
at ij.Executer.runCommand(Executer.java:152)
at ij.Executer.run(Executer.java:70)
at java.lang.Thread.run(Thread.java:750)
Message 2:
java.lang.NullPointerException
at mcib_plugins.Hysteresis_Thresholding.run(Hysteresis_Thresholding.java:43)
at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:266)
at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:114)
at ij.IJ.runUserPlugIn(IJ.java:246)
at ij.IJ.runPlugIn(IJ.java:210)
at ij.Executer.runCommand(Executer.java:152)
at ij.Executer.run(Executer.java:70)
at ij.IJ.run(IJ.java:326)
at ij.IJ.run(IJ.java:416)
at ciliaQ_Prep_jnh.canny3d_thresholder.Processing.doProcessing(Processing.java:50)
at ciliaQ_Prep_jnh.CiliaQPrepMain.segmentUsingCanny3D(CiliaQPrepMain.java:1437)
at ciliaQ_Prep_jnh.CiliaQPrepMain.run(CiliaQPrepMain.java:567)
at ij.IJ.runUserPlugIn(IJ.java:244)
at ij.IJ.runPlugIn(IJ.java:210)
at ij.Executer.runCommand(Executer.java:152)
at ij.Executer.run(Executer.java:70)
at java.lang.Thread.run(Thread.java:750)
For applying the HYSTERESIS threshold, one error messages appears:
java.lang.NullPointerException
at ciliaQ_Prep_jnh.CiliaQPrepMain.doHysteresisThreshold(CiliaQPrepMain.java:1523)
at ciliaQ_Prep_jnh.CiliaQPrepMain.segmentUsingHysteresis(CiliaQPrepMain.java:1486)
at ciliaQ_Prep_jnh.CiliaQPrepMain.run(CiliaQPrepMain.java:580)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:750)
The errors must relate to changes in the 3DSuite library that CiliaQ Preparator uses for performing operations in the segmentation workflows for "HYSTERESIS threshold" or "CANNY3D" since these errors only emerge recently.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.