I have bunch of images of cells from different channels, imageA_c1.tif, imageA_c2.tif and imageA_c3.tif

I wish to clip a bounding box through all the images at the exact same location.

So I imported the 3 images.

Then I align them and group them.

I then set a rectangle at a region of interest on top of these grouped images and then do Path->clip

Clipping is fine.

However, when I ungroup the objects, the clipping is lost and the images revert to their full original size.

Is there a way to retain the crop images using a bounding box through a stack of images and retain them after ungrouping?

Thanks Lee

Hello,
You can use menu Object> Clip > Unset

About Grouping, you can edit the elements of a Group without ungrouping. You have to do a quick double click into the group. It may be confusing, because a slow double clicking it's also interpreted as a transformation (rotate, scale ,etc). And if you click in an empty space, is interpreted as the exit of the group.

Maybe, there is an option in the preferences to change the cliping behavior. I'm not sure .

In the development version, Inkscape 0.49 (now 0.91!), some behaviors have changed. For example the use of the spacebar for moving objects (which I hate!). Maybe you could try there.

EDIT: About your last question, I will say that it's imposible to clip if you ungroup your objects. The SVG format doesn't allow this. They must be grouped.

If you wish to export the svg to png, the image will be resampled and probably blurred thanks to anti-aliasing if the cropping area, the original image's pixels and the render's pixel grid is not matching eachother.
Thus, if you want to make a cristal clean cropping, you may better use gimp instead.

You can open each image on a new layer.
If the area you want to clip is just a rectangle, you can use a simple rectangle select, and then resize canvas to selection, then export each layer to a png.