How to read a binary file in Imagej and the header and plot a 3D data from the binary file in imagej

Dear All,
I tried to load or import .bin file into imageJ and I could not find the exact answer how to load a binary file with 3D data with headers and others comments in it and plot it in 3D or as stack.
I would be very glad if you can help me with this.
There is no option to load binary file in bio-formats.Is there a way to load binary file in imageJ.DOes it support .bin files?

Good day Mike.

Is there a way to load binary file in imageJ.DOes it support .bin files?

I never heard of it and I recommend to save images, image stacks, or general pictorial data in TIF-format.

Which application did produce the data in question?



Hiii @anon96376101,
since I didn’t want to loss information as loading this as image which would result in loss of data/image quality

Sorry but I don’t understand:

Batch processing of what?

What did you save as .bin files?

From which application did you save it?

If you have a raw image file then you need to know the parameters, i.e. the data organization, to open it in ImageJ.

Please be more specific.



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Hii @anon96376101 ,
To be more specific I have some 3D data in file and I know the parameters of the file.But this is not an image file.I want to load this 3D data file into imageJ.
File>import>raw file>… but the problem is that it doesn’t support my .bin file and the 2D data was loaded.

ImageJ is for image processing and as far as I know it treats 3D data exclusively as image stacks.

You may however have a look at the 3D viewer and related plugins that may provide their own data and file organizations.

Personally I’m not familiar with these but perhaps someone in the know will chime in.



Hi @mike123

Note that the dialog after File > Import > Raw...? has a field for Number of images:
which will let you tell imagej how many slices in z there are in your volume.

It would also help if you describe exactly what you filled in for that dialog,
what ImageJ displayed, and how does that differs from what you expected.


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I am having files with edf extension that are collected by SAXS in a synchrotron.

I am trying to open them with imageJ, but the image is not complete.

Can someone help in opening these files



Welcome to the forum.

I recommend you start a new topic post with as much detail as you can about

  1. The file you want to open, how it was aquired and what you mean by “the image is not complete”
  2. What you’ve tried so far to open it


Thanks John for your kind response.

Attached is a picture of what the image looks like

The data has been acquired by SAXS in a synchrotron.

What i did so far i downloaded imageJ and downloaded as much as plugins as i can, some of them for slicing volume data as far as i understand.

Kindly advise.

Thanks and Best Regards

I have done exactly the steps that are mentioned in the forum that you have referred me.

Unfortunately i got the same images.

I tried to upload the files in case you can manage to open them correctly, but they are edf files which are not the allowed format to be uploaded.

Thanks and Best Regards