*Common issues and fixes

Common issues and fixes

Page outlines some common issues that may be encountered due to MATLAB, Fiji, or other quirks specific to the computing environment of calciumImagingAnalysis.

Out of memory using Miji

• If you get a java.lang.OutOfMemoryError: GC overhead limit exceeded style error (see below) when trying to open a movie with Miji, make sure that you initialize MATLAB in the calciumImagingAnalysis path or place the java.opts file in your MATLAB start-up folder.
• This increases the amount of memory allocated so that Java doesn't run out when using Miji to load movies.

java.lang.OutOfMemoryError: GC overhead limit exceeded
	at java.lang.AbstractStringBuilder.<init>(Unknown Source)
	at java.lang.StringBuilder.<init>(Unknown Source)

downloadCnmfGithubRepositories.m not downloading correctly

• If when trying to download using downloadCnmfGithubRepositories.m the below error is encountered, try to run downloadCnmfGithubRepositories several more times as websave (MATLAB built-in function) sometimes momentarily does not obtain the correct write permissions and fails.

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Error using websave (line 104)
Unable to open output file: 'signal_extraction\cnmfe.zip' for writing. Common reasons include that the file exists and does not have write permission or the folder does not have write permissions.

modelPreprocessMovie analysis options list not showing

• MATLAB changed uitables internal implementation, hence findjobj (File Exchange function) broke causing reorderableListbox (File Exchange function) to also break. An updated findjobj has been added to the calciumImagingAnalysis repository and this error (see below) should no longer occur.

Error in reorderableListbox (line 127)
jScrollPane = jScrollPane(1);

Miji not loading correctly

• The below error occurs when the wrong version of Fiji is downloaded. Please 2015 December 22 version download from https://imagej.net/Fiji/Downloads as that implementation of Miji.m appears to work correctly with MATLAB.

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Error using javaObject
No class MIJ can be located on the Java class path

viewMovie or other functions where movies need to be loaded end without executing

• It is likely that the regular expression given to calciumImagingAnalysis does not match any of the files in the folder being analyzed.
• For example, in viewMovie, the below Image movie regexp setting should be changed to concat correspond to the demo raw imaging data's name.

Contrast is low on cell transient ΔF/F movies using computeManualSortSignals

• The contrast (e.g. min/max) are estimated automatically from movie data, but will not always be the optimal display for manual human sorting of data. To improve the contrast, press q while in the interface and adjust the min/max values until you are in a satisfactory range. See below.

Default contrast:

Contrast after user editing:

Blank frames or entire frames baseline shifted after motion correction in modelPreprocessMovie

• This normally occurs when transfturboreg is selected as the registrationFxn, in some Windows editions and OSX versions this leads to random baseline shifts. If this occurs change registrationFxn to imtransform. See below (green selected option).