quantixed / imagej-macros Goto Github PK

Thanks for sharing your tools and adding your update site, @quantixed !

For inspiration, you might want to check out the following projects that offer similar functionality:

1. Figures

   • MagicMontage
   • FigureJ
   • ScientiFig

2. Blind Experiment
   I created this plugin a while ago (release is here). It is supposed to work well with any file type.

If these tools are interesting for you, or you're missing some functionality, it would be great to discuss on the forum how to make them more accessible and useful for the community.

Windows user reports that a mapped network drive doesn't allow the deletion of the temporary files used in the Make Montage (movie) routine.

The best course here would be to generate the temporary files in a local temporary directory. Also, test if junk is left behind in the Temporary directory if/when this is implemented.

at the moment it is working on 600x600 also it only puts RGBM (l-r) no possibility of other montages

Hi Stephen, something is not working for me in Montage_Horizontal_RGB_on_Directory.ijm. When I run it on a folder of 3 color stacks in order to create 3+1 merged panel montages, it stops at line 105 because it's looking for the 4th panel but cannot find any (original stack has 3 slices). I believe that it's because the merged panel hasn't yet been generated yet.

If you add the following lines right before line 98, it now works for me:
mergeString = "c1=[C1-" + tifflist[i] + "] c2=[C2-" + tifflist[i] + "] c3=[C3-" + tifflist[i] + "] keep";
run("Merge Channels...", mergeString);
rename("merge");

Although you still don't have the flexibility of color choice, frame selection, etc that you've successfully implemented in the "flexible" versions of this script.
I'm only using GitHub as a repo for my stuff, I'm not used to the fork/issue/report thingy so please let me know if I'm doing this wrong!

And thank you very much for this script, it's amazing! Following your great example, I'm implementing a way to go from .nd (MetaMorph files) to the source material for your script with correct intensity adjustments handling across many files and conditions.

Blind analysis doesn't remove labels from all channels of a composite image

I successfully used blind analysis last week.
I tried to run it today on my new images, similar but different folder location and it won't rename any image.
I keep getting this error message, but whenever I try to reload the macro, it gives me a different blind number error (assuming with randomisation).
All files are TIFFs, Fiji did update this morning right before I used it so something may have gone wrong there?
I really don't understand coding so have no idea where to start looking

(Note, I have now removed spaces from folder names in case that was an issue for some reason, it didn't help)

Running the code on Windows throws an error on the first run of a menu item. Possibly caused by not lading qFunctions quickly enough. Solution is to just run the code again and it will work (if that is indeed the problem). Code solution would be to write a function which makes the call to load qFunctions. Then the macro can check for execution of the function before continuing.

If a stack is used, without conversion to hyperstack showing channels >1 the macro rejects the stack. If the stack is converted to hyperstack to be multichannel there are LUTs applied that don't work with the single channel montage. Need to force grays onto these.
Also

• incorporate the RGB merge version into the multi version because it's better
• use a single call from the Macros menu to run the macro.

This is probably a new macro but, the ability to add a square ROI to one channel of an existing montage and then have it propagate to other channels and make a blow up in the specified corner.

When placing in Illustrator 72 dpi (default) is a pain. Specify 300 dpi?

Right now, the input is an RGB image and this becomes the merge panel. Flexibility could be added to make the merge whatever, e.g. if we start with RGB, we could end with 3 panels, G, R and merge of G and R.

porting this to a plug-in would make it much faster.

Installation of qFunctions via qStartup in AutoRun fails if a User has a modified startup macro. Since other update sites use this. I need to change the way quantixed macros work.

Changing dpi made me realise that the ability to add a scale bar will be useful.

Test export of 3 panel TIFFs... is border size correct?