Open ctrueden opened 9 years ago
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?
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");
From Ann Wheeler:
Migrated-From: http://fiji.sc/bugzilla/show_bug.cgi?id=1100