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fiji / Colocalisation_Analysis

Fiji's plugin for colocalization analysis
http://imagej.net/Coloc_2
GNU General Public License v3.0
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Input GUI v2: general idea #29

Open chalkie666 opened 9 years ago

chalkie666 commented 9 years ago

make a new input GUI, that is all imageJ2, replacing IJ1 gerneric dialog stuff with however imageJ2 should do, it... swing. Some general inspiration from JACoP would be good.

The Inpu tGUI should deal with settnig all the input parameters, and not bother with eg. images display,

But could display image parameters that are under 1 sec to calculate, eg mean, max, min, and perform the input data sanity checks and show red flags for stuff that is missing or easy/fast to detect as bad.

chalkie666 commented 9 years ago

Yes it's very nice. But we can push it even further

And we can also implement the noise correction method rnbcc ... Should make an issue for that. It might be patented. But that's not always a problem for open source like us. On 11 Aug 2015 20:27, "Ellen T Arena" notifications@github.com wrote:

Have you seen the input GUI from SVI?

https://svi.nl/ColocalizationAnalyzer?highlight=colocalization

it's worth a look-see...

— Reply to this email directly or view it on GitHub https://github.com/fiji/Colocalisation_Analysis/issues/29#issuecomment-130003218 .

etadobson commented 9 years ago

@chalkie666 Ok... another question. i'm new to this whole world so bear with me. currently - the methods that are applied in Coloc2 are pixel-based... unlike with JACoP which also allows for object-based methods... would/could this also be in the pipeline for Coloc2v2??

chalkie666 commented 9 years ago

This is the million dollar question.

Add object based methods or leave that to other tools like in Mosaic update site. Object based methods are doable once try have a good segmentation. But there are no general segmentation methods that work for everything.

Small blobs vs small blobs And Larger extended features vs other stuff Are very different problems.

There are many ways to define colocalisation in objects sense This also a place for things to feature creep out of control. On 11 Aug 2015 23:07, "Ellen T Arena" notifications@github.com wrote:

@chalkie666 https://github.com/chalkie666 Ok... another question. i'm new to this whole world so bear with me. currently - the methods that are applied in Coloc2 are pixel-based... unlike with JACoP which also allows for object-based methods... would/could this also be in the pipeline for Coloc2v2??

— Reply to this email directly or view it on GitHub https://github.com/fiji/Colocalisation_Analysis/issues/29#issuecomment-130077874 .