Re: How to add more than 38 counter types in Cell Counter plugin

Posted by Olivier Burri on Mar 04, 2015; 8:31am
URL: http://imagej.273.s1.nabble.com/How-to-add-more-than-38-counter-types-in-Cell-Counter-plugin-tp5011798p5011858.html

Hi Curtis

> I would still strongly recommend automated or semi-automated counting if
> possible. But if that is truly impossible for some reason, then that is a great
> suggestion.

I agree that some semi-automatic method could be very useful, however images like the ones processed by Pavica tend to have a lot of artifacts and uninteresting objects that are rather difficult to distinguish from useful ones. The only thing that I could think of is finding a way to rougly segment the images initially and then use something like Cell Profiler Analyst to hope and find some features to help classify the critters. The problem there is that without a dedicated image processing analyst the learning curve for a biologist to segment and is a bit steep until we can even assess whether the results are good or not... My two cents

>
> It would help users a lot to use an update site for distribution [1].
> Distributing these things with Fiji is also a nice option [2]; just let me know if
> you want to pursue that.

We do have an update site and we can now pack the actionBars into JAR files. I just did not think it would be so relevant in this case (I did write it in 30 minutes). But I could put it on GIT or in a GIST if you thing that would be useful. It is just macro code in the end, not a full plugin...

> [1] http://imagej.net/Distribution
> [2] http://fiji.sc/Fiji_contribution_requirements

Thanks a lot for the references!

Regarding update sites, our group has one now and we have a few plugins and actionbars on it. The problem I have now is that as we start producing more and more tools, having them all in the same update site makes it a bit bulky, as not all users want to get all our tools. Is there some suggestion as to how to address this? Should we split our packages in different update sites, for example?

Thanks again and all the best

Oli



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