Skip to content, Skip to search

Changes

Coloc 2

431 bytes added, 11:54, 8 August 2015
Ideas List: put links to commits for fixed issues and make 2 sections, fixed stuff and ideas.
Please see the [[Colocalization Analysis]] page for further discussion of precautions.
 
== Newly added features and squashed bugs ==
The definitive list of new features and fixes is the source code history as shown by the GIT history here: https://github.com/fiji/Colocalisation_Analysis/commits/master
This is just an easy to check, casual list for users, and might not be up to date.
These might not all be in the version of the Coloc_2 plugin released into the imageJ/Fiji updater; you can see that version listed in the updater.
 
New after version 2.0.2, hopefully going into version 2.0.3:
# 08-2015 Fixed in fiji master github repo by commit https://github.com/fiji/Colocalisation_Analysis/commit/492b846c032bd85651ffce7b52c96b3520eff6bb:
## if 2D histogram regression finds a y intercept that is below zero it gives the too high warning "Warning! y-intercept high - The absolute y-intercept of the auto threshold regression line is high. Maybe you should use a ROI, maybe do a background subtraction in both channels" So should change warning text to too high or too low depending on if its positive or negative.
# 08-2015 Fixed in fiji master github repo by commit https://github.com/fiji/Colocalisation_Analysis/commit/4cfc8861f05f277075c3fb7881ebf0d7e54c67c3:
## Numerical results and image stats are currently spewed into the IJ.log window. This is done separately from the way results are put into the simple results display window or the PDF output. So there three differently formatted results outputs with different stuff in them. Different ResultsHandler implementations like PDF or Simple can and do show a different selection of results. This is over complicated, so it should be made into one thing, that outputs the same numerical results and stats values, in the same order in all ResultsHander implementations: GUI display and PDF output, and also the IJ.log. Can reuse the ValueResults class for all three by doing the same thing in each.
### commit https://github.com/fiji/Colocalisation_Analysis/commit/a493b2c88a14f4f6403451aeee6989bf7a2becfb Make IJ.log writing only happen once and only in the default ResultHandler that's always used.
### commits https://github.com/fiji/Colocalisation_Analysis/commit/e833597d7d8a7b4d3db747512f6048d67d61d120 and https://github.com/fiji/Colocalisation_Analysis/commit/75184e88cd6c1e0914ec87caebe97494002bcd4e Get the Coloc job name from the DataContainer image names, and also add the mark/ROI ID to the job name in case there are multiple ROIs.
# 08-2015 Fixed in fiji master github repo:
## Running as imageJ macro command fails because of the parameter: show_"save_pdf"_dialog. Probably the "" are messing up the run(Coloc_2, "params"); text string parameters. So need to get rid of the "" around save_pdf.
== Ideas List ==
The items below will be moved to the issue tracker or design document as appropriate.
# Bug tracker issue no.17 Add Tests and implementation for %Colocalization by intensity and pixels(or voxels) wrt each channel, as per the depreciated Colocalization Threshold plugin - force use of a ROI or mask, as only then do these measures make sense. Add docs for this.
# Missing Feature?: implement flags in GUI to turn on and off desired output values??? Or does this break the idea of having a standardized output? Perhaps instead just make sure the IJ.log output is easily parse-able by humans and machines.
# Bug: Large images don't fit in results display gui, and there are no scroll bars.
# Enable use multi-channel images as well as the current 2 images (one channel each) plus 1 mask image selection. Need to choose which images in the multi-channel images if there are more than 2.... or even which 2 channels and which mask images, if the multi-channel image contains 3 or more channels. This avoids the user having to run split channels. Ease of use.
# Running as macro need a method / GUI parameter to make the PDF file output saved without user interaction.
# Running as macro command in a loop, need to use macro commands to save the IJ.log window results, then clear the log window before the next set of results are sent there. Add words to documentation to explain that.
# Fixed in fiji master github repo trivial bug:
## if 2D histogram regression finds a y intercept that is below zero it gives the too high warning "Warning! y-intercept high - The absolute y-intercept of the auto threshold regression line is high. Maybe you should use a ROI, maybe do a background subtraction in both channels" So should change warning text to too high or too low depending on if its positive or negative.
# Fixed in fiji master github repo:
## Numerical results and image stats are currently spewed into the IJ.log window. This is done separately from the way results are put into the simple results display window or the PDF output. So there three differently formatted results outputs with different stuff in them. Different ResultsHandler implementations like PDF or Simple can and do show a different selection of results. This is over complicated, so it should be made into one thing, that outputs the same numerical results and stats values, in the same order in all ResultsHander implementations ( GUI display and PDF output, and also the IJ.log. Can reuse the ValueResults class for all three by doing the same thing in each ".
### Make IJ.log writing only happen once and only in SimpleWindowDisplay - the default ResultHandler that's always used.
### get the Coloc job name from the DataContainer image names, and also add the mark/ROI OD to the job name in case there are multiple ROIs.
# Fixed in fiji master github repo:
## Running as imageJ macro command fails because of the parameter: show_"save_pdf"_dialog. Probably the "" are messing up the run(Coloc_2, "params"); text string parameters. So need to escape out or get rid of the "" around save_pdf... why are they there? Just to look nice apparently?
== DONE ==