Opening Images from Command Line or Python

Posted by rfor10 on Nov 22, 2016; 4:41am
URL: http://imagej.273.s1.nabble.com/Opening-Images-from-Command-Line-or-Python-tp5017611.html

Hi - I do image analysis in python, but haven't found a great 3D image viewer for my images. I really like ImageJ for that, but I have had some trouble figuring out how to open some images in ImageJ programmatically.

I thought I would be able to temp save an image and issue a system call from python along the lines of

java -Xmx512m -jar ~/ImageJ/ImageJ.app/Contents/Resources/Java/ij.jar -ijpath /ImageJ/ImageJ.app/ ~/Image/acq_4/img_000000000_581_000.tif

When I do this ImageJ loads, but throws an error "File is not in a supported format, a reader plugin is not available, or it was not found."

Any suggestions? Or alternate approach for opening an image in ImageJ from python?

Thanks!