Posted by
ctrueden on
Mar 02, 2015; 9:54pm
URL: http://imagej.273.s1.nabble.com/How-to-add-more-than-38-counter-types-in-Cell-Counter-plugin-tp5011798p5011832.html
Hi Pavica & Romain,
> Will be doable to have editable name for each counter ?
I added the Cell Counter plugin to the Fiji distribution of ImageJ [1].
Find it in the Plugins > Analyze menu (or better: press L to easily launch
plugins).
I forked the code from the version on the ImageJ1 web site, cleaned up and
updated the code.
I added a simple Rename feature for renaming the counter types.
Unfortunately, I did not have time to make it save the new labels when
saving XML etc.
I also investigated adding a scroll bar to the counter types (you'd think
it would be easy), but was not able to do it with reasonable effort because
the code uses a complex "grid bag" layout. It would take at least some
hours to migrate the code away from that type of layout, so that a scroll
bar could easily be added.
At least now the code is on GitHub [2], so that others can easily
contribute such enhancements if they have time.
Finally, I would strongly urge those using this plugin to seek a more
automated way of counting your structures, especially if you need more than
38 (!!!) counter types. You really want to find a way to make your
published results reproducible, in the name of good science [3].
Regards,
Curtis
P.S. to the original author (Kurt De Vos): let me know if you want to be
added as an admin on the GitHub repository.
[1]
http://fiji.sc/Cell_Counter[2]
https://github.com/fiji/Cell_Counter[3]
http://loci.wisc.edu/software/ossOn Fri, Feb 27, 2015 at 2:19 AM, Guiet Romain <
[hidden email]> wrote:
> Hi Pavica,
>
> I don’t have a direct solution to your problem, but it reminds me one
> concern I had a few weeks ago (and that I overcame by a different way) and
> thus I take advantage of your thread to make a suggestion of a new feature
> to the CellCounter developper…
>
> Will be doable to have editable name for each counter ?
> Using a text field (maybe limited in size).
> If this configuration could be save and load (in text/csv file), it will
> be even more usefull.
>
> Cheers,
>
> Romain
>
>
> ---------------------------------------------------------------
> Dr. Romain Guiet
> Bioimaging and Optics Platform (PT-BIOP)
> Ecole Polytechnique Fédérale de Lausanne (EPFL)
> Faculty of Life Sciences
> Station 19, AI 0140
> CH-1015 Lausanne
>
> Phone: [+4121 69] 39629
>
http://biop.epfl.ch/> ---------------------------------------------------------------
>
> ________________________________________
> De : ImageJ Interest Group [
[hidden email]] de la part de Pavica [
>
[hidden email]]
> Envoyé : vendredi 27 février 2015 08:29
> À :
[hidden email]
> Objet : How to add more than 38 counter types in Cell Counter plugin
>
> Hi,
>
> I analyze invertebrate diversity on bottom-ocean images and I find many
> invertebrate species on each photo. However, I can only add up to 38
> counter
> types in the Cell Counter plugin since the number of the counter types that
> fit on the screen depends on the size of my computer screen (!?) from the
> top to the bottom of the screen. You can imagine that I am using the
> biggest
> screen I can find.
>
> I am wandering whether anyone ran into this problem and maybe solved it by
> fixing the plugin so that you can scroll up and down the cell counter
> window, once you ran into the bottom of the screen.
>
> I really probably need around 200 counter types, since I have several
> stations and the species only partially overlap between the stations. So
> far, I have been assigning Types 1-38 for different species at each station
> but this eventually leads to a major confusion and a lot of additional work
> on data editing.
>
> Thank you,
>
> Pavica
>
>
>
> --
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