search

zitmen / thunderstorm

ThunderSTORM: a comprehensive ImageJ plugin for SMLM data analysis and super-resolution imaging
http://zitmen.github.io/thunderstorm/
GNU General Public License v3.0
91 stars 42 forks source link

Issue with running PSF Elliptical Gaussian 3D astigmatism analysis #74

Closed 3DSTORMenthusiast closed 8 months ago

3DSTORMenthusiast commented 10 months ago

New issue (ran same analysis without issues a few weeks ago) with running analysis for PSF Elliptical Gaussian 3D astigmatism - I ensured that the latest version of Thunderstorm was installed, increased the memory limit (tried on two separate computers with 8GB and 16GB RAM), and tried running analysis after importing the tif as a virtual stack but continue to receive the following exception:

(Fiji Is Just) ImageJ 2.14.0/1.54f; Java 1.8.0_322 [64-bit]; Mac OS X 10.16; 216MB of 6222MB (3%)

java.lang.OutOfMemoryError: Java heap space at ij.process.FloatProcessor.(FloatProcessor.java:38) at cz.cuni.lf1.lge.ThunderSTORM.rendering.AbstractRendering.(AbstractRendering.java:230) at cz.cuni.lf1.lge.ThunderSTORM.rendering.ASHRendering.(ASHRendering.java:15) at cz.cuni.lf1.lge.ThunderSTORM.rendering.ASHRendering$Builder.build(ASHRendering.java:55) at cz.cuni.lf1.lge.ThunderSTORM.rendering.ui.ASHRenderingUI.getMethod(ASHRenderingUI.java:73) at cz.cuni.lf1.lge.ThunderSTORM.rendering.ui.AbstractRenderingUI.getImplementation(AbstractRenderingUI.java:181) at cz.cuni.lf1.lge.ThunderSTORM.rendering.ui.AbstractRenderingUI.getImplementation(AbstractRenderingUI.java:21) at cz.cuni.lf1.lge.ThunderSTORM.AnalysisPlugIn.showDialog(AnalysisPlugIn.java:170) at ij.plugin.filter.PlugInFilterRunner.(PlugInFilterRunner.java:63) 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 java.lang.Thread.run(Thread.java:750)

Attached are the settings I use to run my analysis. Settings

Would be happy to hear any more advice about how to get this analysis to work again! My image processing prior to running Thunderstorm is unchanged.