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How to install BioFormatsLink

Posted 1 month ago

I want to import a *.spc file that my spectrometer creates.

I understand that I need to install the BioFormatsLink package. Downloading the repository and extracting the files to /home/myusername/Downloads/BioFormatsLink-master/, I double clicked the file PacletInfo.wl. Then Mathematica opened and I clicked "Run Package".

I now see the following:

enter image description here

Has the package been installed? Where is the paclet file located now? Or should I run another command?

POSTED BY: Ehud Behar
2 Replies

What you did, opening the .wl file in the front end and hitting "Run Package", is not the correct way to load an external package. On top of that, the file you opened is the paclet info file, which doesn't really have any executable code so 'running' it doesn't do anything (and therefore doesn't give you any helpful error messages that you've done something wrong).

The instructions on the github page give a few methods for installing the package, did you try them and have issues? I think you can just run

PacletInstall["BioFormatsLink"]

and it should install.

POSTED BY: Jason Biggs
Posted 1 month ago

Thank you for reply.

I just run PacletInstall["BioFormatsLink"], and then went on to check if the package is installed: I tried to Import a file as described in the example here:

file = URLDownload["http://downloads.openmicroscopy.org/images/NIfTI/NIH/zstat1.nii","zstat1.nii"]
Import[file]

and got the message Import::fmterr: Cannot import data as BioImageFormat format. Is there a more systematic way of telling whether the package is installed and ready to use?

POSTED BY: Ehud Behar
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