Exporting transformed image in BigWarp with correct resolution

Hi,

I’ve been using bigwarp to align TEM images with confocal images, but I’m having trouble exporting the fused image after alignment with the resolution of the TEM image. I’m using the TEM as a moving image and the confocal as target image, both 8-bit TIFFs.

When trying to export the moving image using File->Export as ImagePlus it gives me the options to export the resolution and field of view with either the moving or target image, but after trying out all different options and combinations I can’t seem to get the resolution from the TEM moving image to the exported image.

I’ve then tried this script from the ImageJ homepage to get the moving and target image aligned using my landmarks (bigwarp/Apply_Bigwarp_Xfm.groovy at 90cc95f5fe5cf01408a42b292b195d31ff866acf · saalfeldlab/bigwarp · GitHub) but I get an error message “Undefined variable in line 8”. I’ve also tried just capturing the transformed image from ImageJ utilities menu, but it doesn’t work either (won’t register bigwarp windows while using the plugin)

I’m sure the solution to my problem is simple and there is something I’m missing here…

Kind regards,
Martin

1 Like

Hi @Martin.S

Welcome to the forum!

I can’t seem to get the resolution from the TEM moving image to the exported image.

Can you explain what you mean here? You want to fuse TEM and confocal images. I understand this to mean that you want two images: 1) confocal, 2) transformed TEM, such that the two images are aligned, the same size, and at the same resolution. Is that correct?

Since you say you want to export

the fused image after alignment with the resolution of the TEM image

I understand that you want the fusion to be at the TEM resolution. If the above are all correct, this means you need to upsample your confocal image.

Your TEM and confocal images be different sizes and still be aligned if their resolutions are different, but I’m not sure if that’s what you want or need.

Other follow up questions:

  • What are the sizes and resolutions of your TEM and confocal images?
  • Are the resolutions you expect reflected in your image metadata?
    • You can check with Help > Show source information in the newest BigWarp (7.0.1)

You should be able to do what you want with the Bigwarp plugin alone now (and not need that script, which is out-of-date*). Once I’m sure I understand what you’d like to do, I’ll be happy to help get you a solution.

John

*updating the Bigwarp page on the ImageJ wiki is tricky right now yet due to maintenance. I will change the info there as soon as the new website is ready).