Comstat install issues




I have a mac (high sierra, 10.13.4) and have installed comstat as recommended in the manual provided by them. I don’t have any other installations of ImageJ on here.

The ImageJ file opens fine, but comstat is not shown in the plugins menu. The files comstat2_.jar, comstat2.ini and loci_tools.jar are in the plugins folder.

I also cannot open .lif files (from leica sp5 confocal microscope) which I should be able to with loci tools, but not sure if thats related to comstat or a separate issue. Any suggestions?

Thanks in advance



Sorry - but I do not know the Comstat tool at all. On their page - they have a contact email: Perhaps it’s worth contacting them directly regarding your current issues?

And yes - we recommend opening images using Bio-Formats. If you are using Fiji - which we recommend - you can simply go to File > Import > Bio-Formats - that should open you .lif file without issue.

If you have other questions - please do ask. We are here to help!



Hello there.

Comstat2 does not like Fiji, so we do not recommend to install it in an Fiji environment.

Regarding the missing plugins - I have heard that several times lately, so perhaps it is a High Sierra related issue.

Try to remove your ImageJ/Comstat installation - or leave it where it is.

Install a new copy from the install file by dragging the Comstat2 folder to the desktop (not the Programs folder) and start ImageJ from that new Comstat2 folder. You will most likely get a warning before you can start ImageJ. Usually you can just accept the bypass on the warning dialog, or if there is no bypass go back and try to right-click on the ImageJ icon and chose “Open”.

Hopefully this will solve the problem.

Good Luck

(one of the Comstat team at Tech U of Denmark)


Thanks @comstat for joining in and providing advice!

Is there any reason for this? Are there incompatibilities with other plugins shipped by Fiji?

I think it would be much easier for users if they could simply activate an update site to get ComStat2 installed, without having to care about third-party dependencies and other possible issues. The ImageJ developers and the community of this forum would certainly be happy to assist with setting up an update site :slight_smile: