Thanks for BaSiC which generally works awesome. However we sometimes find issues when processing fluorescence images from plates with sparse cells. I'm under the impression that there are two potential pitfalls for BaSiC:

• If the cells are sparse and small, the imresize() may not capture them at all? It will use nearest neighbor, as far as I could see, so it may just happen to not grasp the relevant foreground pixels?
• The model from BaSiC is sometimes quite irregular, with strong local variations, i.e. in cases of dirt or sparse cells. I think it would help to regularize more strongly, but I do not know how to sensibly do that in the code. Actually I am often under the impression that a resolution of 32x32 instead of 128x128 would be sufficient, but I do not feel comfortable to change such integral settings of the method. Do you have recommendations for regularization of the model?

Hi, I ran the demo examples WSI brain Matlab code and error was occurred like below:

Unrecognized function or variable 'BaSiC'.

Error in example_brainWSI (line 14) [flatfield,darkfield] = BaSiC(IF,'darkfield','true');

I installed the BaSiC plugin as outlined and have used it before on Fiji. Recently I tried to use it again and it hit the following incompatibility. I don't know where to start from in troubleshooting.

[Sun Oct 03 17:30:57 CEST 2021] [ERROR] [] null java.lang.NoSuchMethodException: Could not find method edu.emory.mathcs.utils.ConcurrencyUtils.getThreadsBeginN_1D()I There was a problem with the class edu.emory.mathcs.utils.ConcurrencyUtils which can be found here: /Users/work/Applications/Fiji.app/jars/jtransforms-2.4.jar /Users/work/Applications/Fiji.app/jars/parallelcolt-0.9.4.jar

WARNING: multiple locations found! java.lang.NoSuchMethodError: edu.emory.mathcs.utils.ConcurrencyUtils.getThreadsBeginN_1D()I at cern.colt.matrix.tdouble.impl.DenseDoubleMatrix1D.zSum(Unknown Source) at BaSiC_.matrixMean(BaSiC_.java:1041) at BaSiC_.ShadingCorrection(BaSiC_.java:540) at BaSiC_.exec(BaSiC_.java:403) at BaSiC_.processDialog(BaSiC_.java:259) at BaSiC_.showDialog(BaSiC_.java:164) at BaSiC_.run(BaSiC_.java:113) at ij.IJ.runUserPlugIn(IJ.java:241) at ij.IJ.runPlugIn(IJ.java:204) at ij.Executer.runCommand(Executer.java:150) at ij.Executer.run(Executer.java:68) at java.lang.Thread.run(Thread.java:748)

at cern.colt.matrix.tdouble.impl.DenseDoubleMatrix1D.zSum(Unknown Source)
at BaSiC_.matrixMean(BaSiC_.java:1041)
at BaSiC_.ShadingCorrection(BaSiC_.java:540)
at BaSiC_.exec(BaSiC_.java:403)
at BaSiC_.processDialog(BaSiC_.java:259)
at BaSiC_.showDialog(BaSiC_.java:164)
at BaSiC_.run(BaSiC_.java:113)
at ij.IJ.runUserPlugIn(IJ.java:241)
at ij.IJ.runPlugIn(IJ.java:204)
at ij.Executer.runCommand(Executer.java:150)
at ij.Executer.run(Executer.java:68)
at java.lang.Thread.run(Thread.java:748)

Hi. I'm trying to call basic during ImageJ headless execution, but I get the error message in the title.

ImagePlus stack = FolderOpener.open(currentChannelPath);
stack.setTitle("Stack.tif");
IJ.run(stack, "BaSiC ", "processing_stack=Stack.tif flat-field=None dark-field=None shading_estimation=[Estimate shading profiles] shading_model=[Estimate flat-field only (ignore dark-field)] setting_regularisationparametes=Automatic temporal_drift=Ignore correction_options=[Compute shading and correct images] lambda_flat=0.50 lambda_dark=0.50");

Then I get the error, even though the stack is opened. I run ImageJ from the command line using --headless and call the script above during excecution. Would greatly appreciate any help!