opening SCN file in MATLAB

I have downloaded the Bio-Formats zipped folder bfmatlab and unzipped on my MATLAB path. But I still can't use function bfopen().The error information as pictures.

[Walter Roberson]

I would experiment with renaming the file so that it did not have periods in the name except before scn

Answer 1

[Priysha LNU]

Hi,

Please check the version of the Bio-Formats library being used by the following command:

disp(char(loci.formats.FormatTools.VERSION))

If this results in the following isse,

Undefined variable "loci" or class "loci.formats.FormatTools.VERSION".

then the Bio-Formats JARs are not on the Java classpath. If you have downloaded the latest Bio-Formats MATLAB toolbox, you should be able to put these JARs on the classpath and return the version of the library via:

[status,version] = bfCheckJavaPath()

Having performed these operations, please try re-running the toolbox function:

data = bfopen('<filename>.scn');

If there is still an error, please consider renaming the '.scn' file to a string which does not contain any characters (.,/?<>:;'"*&^%$#@<space>) and try re-rerunning the command.

DISCLAIMER: These are my own views and in no way depict those of MathWorks.

[lin ai]

Thanks for your answer! I have tried your solution that changed the file name to "try.scn" and re-running the function "bfopen". But it still return me this error. And I ran the sentence "[status,version] = bfCheckJavaPath()", and it also gave me the right answer but not give me the error information. So what should I do next?

[Walter Roberson]

Would it be possible to zip try.scn and attach the zip, for our testing purposes?

[lin ai]

Sorry, it's not convenient to give you the file. Maybe is it the version of MATLAB and the version of Bio-Formats not matched? I used MATLAB2020 and Bio-Formats6.5.1. If so, could you tell me the successful match of MATLAB and Bio-Formats? Thank you so much.

[JSC]

I know this is months later, but it looks to me like the issue is that you named your file "try. scn" with a space after the period, instead of "try.scn" without a space.