R2021a

[Pablo1990]

Dear @rbonazzola @tvmendonca,

Thank you for developing this project, is really cool! Still, I've been trying to use it, but I have encounters a few barriers:

README:

• 'Add the folders with subfolders for the Origami scripts to the MATLAB search path', I don't know if this is completely necessary (I think it worked without adding them). Still, if necessary, you could also add them automatically like (e.g.):
  addpath(fullfile(pwd,'functions'));
• https://wiki.med.harvard.edu/SysBio/Megason/ACME - It states a 403 forbidden access

Matlab R2021a

• When I try to run the pipeline from scratch, at first it only accepts '.mha' files. If remove '*.mha' from line 55 of 'OrigamiPipeline_Main.m', it now accepts only tifs.
• I select a tif that I have from PlantSeg (https://github.com/hci-unihd/plant-seg) and I get the error: ' Unrecognized field name "ImageDescription".'

Many thanks again!
Pablo

[tvmendonca]

Hi Pablo

Thanks for getting in touch! I'll have a look at the issues and try to get back to you later this week. :)

Cheers
Tania

[tvmendonca]

Hi Pablo,

Sorry it's taken me a while to get back to this!

• The readme file has been updated and should refer to the Github page for ACME now and not the broken link: https://github.com/krm15/ACME/wiki

• The file dialogue box defaults to .mha but you should be able to select one of the other filetypes supported (.tif, .obj, .mat) by changing the filetype in the file dialogue dropdown list
  

• I have unfortunately seen that error when the image header in the tiff is missing the necessary tiff tags or if it is corrupted which means imread would not work. A not very elegant work around is to open the tiffs in ImageJ and re-save which I found repairs the tiff header. Hope this helps!

Best
Tania