Bio-Format (saveas .ome.tif) XYZCT reading

I open nikon image timeseries file (.nd2) file using Bio-Format import in ImageJ. Then, I saved the t-series as .ome.tif using ‘saveas’ in ImageJ. Afterwards, when I open the saved t-series (.ome.tif) file using standard ImageJ’s ‘open’ function, the number of frames is read as z-stack size (image properties). I donot understand how dimensionorder XYZCT is altered.

@debanjan.goswami do you open the .ome.tif image with Bio-Format? If so, you can change the stack order by changing “view stack with” to “standard ImageJ” and change the “stack order” to the order you need.

When you open the first (original .nd2) image does ImageJ recognize the right stack order?

@NoUsername Thanks for your prompt response. Your’re right by saying that I can always change the dimensionorder manually. The steps I am taking is little more lengthy than that of the way I phrased it here. I use script in Matlab for this purpose and 'bfopen' function is working fine and recognizing the XYZCT in correct order. Afterwards I save the imagestack (t-series) using 'bfsave' save the metadata in .ome.tif format. The reason I want this t-series to be read by ImageJ’s original function, called ImagePlus, is to gain the ability to use TrackMate script in my final Matlab code.

Ant insight to correct this matter will be very helpful for me.

BTW, the faulty reading of .ome.tif t-series file seems to be gone after I activated the IJ2 (SCIFIO) in my FIJI version. But the problem remains when I use ImagePlus fucntion in Matlab code. I think, I need to update the library with new library. I dont know where and how.

Thanks again,

Looking forward for solutions of this issue.


@debanjan.goswami I’m not very familiar with Matlab. But as I understand you use the “normal” import function. You could try to use the Bio-format plugin to open Images. I’m not sure if this plugin also opens images with the type ImagePlus (I’m just a beginner in programming, so you should have more knowledge about this).