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imodpasteur / ZOLA-3D

Zernike Optimized Localization Algorithm for 3D single molecule localizations
GNU General Public License v3.0
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Error when using sCMOS corrections #7

Open dpshepherd opened 5 years ago

dpshepherd commented 5 years ago

Thanks for all of the hard work on ZOLA! We have a question because we are running into an error when using sCMOS correction.

We are running ZOLA-3D on Windows 7 Pro 64-bit, ImageJ 1.52n, and Java 8.

Using a stack of PSFs we are able to successfully run Calibration: PSF modeling, using the GPU/CUDA 10, if we choose the Camera setup: EMCCD option for the camera. However, when we choose Camera setup:sCMOS and provide ZOLA-3D with the file paths for three needed files (16-bit TIFFs for offset, variance, and gain) that we normally utilize for fitting with the Huang et al algorithm in MATLAB, we get the following error:

(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52n; Java 1.8.0_131 [64-bit]; Windows 7 6.1; 1272MB of 96000MB (1%)

java.util.regex.PatternSyntaxException: Unexpected internal error near index 1 \ ^ at java.util.regex.Pattern.error(Pattern.java:1955) at java.util.regex.Pattern.compile(Pattern.java:1702) at java.util.regex.Pattern.(Pattern.java:1351) at java.util.regex.Pattern.compile(Pattern.java:1028) at java.lang.String.split(String.java:2380) at java.lang.String.split(String.java:2422) at org.pasteur.imagej.ZOLA.calibration(ZOLA.java:1862) at org.pasteur.imagej.ZOLA.run(ZOLA.java:340) at ij.IJ.runUserPlugIn(IJ.java:229) at ij.IJ.runPlugIn(IJ.java:193) at ij.Executer.runCommand(Executer.java:137) at ij.Executer.run(Executer.java:66) at java.lang.Thread.run(Thread.java:748)

I have tried to change the file delimiter to '\', \', '\\', and '/' with no success. Any suggestions?

Thanks!

benoitbenoit commented 5 years ago

Hello, Could you try the new version please : ZOLA-0.2.4 ? You can download it here https://github.com/imodpasteur/ZOLA-3D/releases/download/2.4/ZOLA_-0.2.4-SNAPSHOT.jar or update it using Fiji update site. Thanks, Benoit

dpshepherd commented 5 years ago

Hi Benoit,

The Calibration: PSF modeling window now loads, but it is not working correctly for sCMOS.

First, the offset and variance file paths are switched somewhere. image

Second, if I manually switch the offset and variance paths, the calibration initializes and then immediately exits without generating a PSF fit. image

ZOLA version: 0.2.4-SNAPSHOT ZOLA PSF modeling started initialization started initialization 1/6 initialization 2/6 initialization 3/6 initialization 4/6 initialization 5/6 initialization 6/6 calibration started iteration: 0/30 calibration finished residual (0) : NaN global residual : NaN calibration file saved elapsed time 0.0 min 5.0 sec

If I run calibration using the same bead image with the camera set as an EMCCD (using values averaged over the entire sCMOS chip), we obtain a reasonable result using Calibration: PSF Modeling.

I can provide the bead images and sCMOS characterization images via Dropbox if it would be helpful?

Thanks, Doug

benoitbenoit commented 5 years ago

Indeed, having data in a dropbox folder could help me resolving this bug. Could you share it with me please ? My email address is the following: benoit.lelandais@pasteur.fr (I am quite busy currently but I will try to solve this bug during the next few weeks.) Thank you