Need help saving an image in imageJ through MIJI/MATLAB Interface

I feel like this is such a simple task but I cannot for the life of me figure out how to just save the stitched image Fiji produces for me. I can tell the program to run through the plugins and do the stitching but after that I just want to save and close the image and move on to the next loop iteration and not bog down the memory. I have tried using the MIJ.run command and doing something like:

MIJ.run('saveAs', 'Tiff..., path=[F:\\4_19_16\\LB598_LL_2_3_4_5\\XY01\\x.tif]');

But the MATLAB doesn't like what I am telling it to do and says that "SaveAs is an unrecognized command". Does anyone know how to do this? I appreciate any help. It does it for both save and save as.

Answer 1

[Sergey]

Use Save instead

MIJ.run('Save', 'Tiff..., path=[F:\\4_19_16\\LB598_LL_2_3_4_5\\XY01\\x.tif]');

[Shui Hu]

This doesn't give an error. But it doesn't seem to actually save it. I can see that ImageJ is processing the command, but no file appears in the given directory. Nor does it overwrites the original image. Does it work for you?

[Fabian Arns]

For me the command worked. Thx a lot!

However I needed to refresh the destination folder before it was shown.

[raym]

it does not work on my computer

[PaulB]

Hello,

The 'Save' command given by Sergey did work, but it does not allow to change the name of the file. This command overwrite on the image file, which i don't want.

I used this command :

MIJ.run('Save','Tiff..., newName');

where newName is a contatenated String variable composed of the initial image name and '_crop'.

EDIT : I did found a workaround using the Duplicate command :

MIJ.run('Duplicate...', strcat('title=[', newName, ']')) ;

MIJ.run('Save','Tiff...') ;

An ImageJ 'Save' dialog box then appears, you just have to hit Enter.

Answer 2

[sorly]

Hi,

It seems this works for me:

MIJ.run('Tiff...','path=[newName]');