Input GUI v2: and Results: Improve scriptability

[ctrueden]

From Ann Wheeler:

This all needs to be scriptable so if one has 100 - 200 images Fiji can munch through them and generate an results file exportable to Excel with:

Columns corresponding to:

Slice, ROI, Threshold, 'My favourite colocalisation coefficient', 'Other colocalisation coefficient', 'AN OTHER parameter as desired'

Rows corresponding to:
Slice 1, ROI1
Slice 1, ROI2
Slice 2, ROI1
Slice 2, ROI2 etc

Not dissimilar to the output of multimeasure for analysing particles. Manders Coefficient and ICQ in IJ1 can do all of this and are scriptable easily.

Migrated-From: http://fiji.sc/bugzilla/show_bug.cgi?id=1100

[chalkie666]

for getting results for different slices of a stack, the user should do the analysis slice by slice, using the batch macro processor on a a directory of single slice images with a z slice ID in the filename
If we allow single slice results output for a z stack, there could be hundreds of output values per image stack.... From a macro/batch/scale up standpoint, its possibly best to have one output results file per analysis job, with a unique filename, so its easier to wrangle the data later in R or whatever.
What Ann proposed makes sense superficially, but might end up hurting in a large scale analysis?

[chalkie666]

further to the above.... i cant see how we can currently run coloc_2 using eg process-batch-macro since coloc2 needs 2 or 3 images as parameters.... how can we make this easy? is there a general tool in imagej to specify multiple sets of files as input parameters for a macro command of the case like
run("pluginname", "parameter1 parameter2 parameter3......");
????

we have a whopper of a macro command in this case:
run("Coloc 2", "channel_1=[clown.jpg (red)] channel_2=[clown.jpg (green)] roi_or_mask=[clown.jpg (blue)] show_save_pdf_dialog display_images_in_result display_shuffled_images li_histogram_channel_1 li_histogram_channel_2 li_icq spearman's_rank_correlation manders'_correlation kendall's_tau_rank_correlation 2d_instensity_histogram costes'_significance_test psf=3 costes_randomisations=10");