Rescaling and aligning different images

I have these two pictures:

I would like to, if possible, rescale and stitch automatically both images.

Hi Mario,

Does it need to be automated for lots of images?

I have attempted a few automated methods, but they come up short. I feel the best method is to use landmarks that have been set manually.

A method that worked fairly well for me, was the “Align by line ROI” plugin, followed by copying of the higher mag. image on to the lower one as an overlay (including zeroes as transparent in the settings). This relies on landmarks, such as the scratches in the centre, the lines can be used for both scale and rotation. Make sure the higher mag. image is the target, so the low mag. image is scaled up.

Alternatively, if the files contain metadata of the pixel size, or a way of calculating it (e.g. from the magnification/pixels), then you could use that to automatically scale them. Then use a registering plugin like StackReg/TurboReg to align them. Again, copying as overlay to finish off. Another alternative, would be to set the scale manually using the scalebars provided, then scale up the low mag. image and do an automated registration after that.

Best,

Rob

EDIT: i have realised that there is some oversight with my method, the canvas size restricts the rest of the information in the low mag. image. Therefore there are some tweaks needed with this method, i will attempt them tomorrow.

EDIT2: the images should have their scale set (Analyse -> Set scale…) using a line ROI to trace the scalebars. The pixel size can then be found in the properties (Image -> Properties) and the ratio used to scale the lower mag. image. After this, the smaller image canvas must be increased in size (I copied it in to a new window) and then I used the Align by line ROI plugin with no scaling/rotation to register the two images. Unfortunately StackReg doesn’t seem to work, the grayscale values seem a bit off between the images, which might explain it. Finally I copied the image as an overlay - however it might be possible to use MosaicJ to merge the images.