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ImageJ has a simple and effective tool for Straightening images of curved structures, which can be found in the menus as Edit › Selection › Straighten…. A silly example (straightening an MPI canteen banana) is shown here.
First, select the “Segmented Line” selection tool by right-clicking on the “Straight Line Selections” tool icon in the toolbar and choosing the “Segemented Lines” option. Then click along a selection of points along the structure, completing the line with a right click. You should have something like this:
Then select the Edit › Selection › Straighten… menu option and you should be prompted for a line width - this determines the width around the line you’ve drawn that will be used in the final image. In this case, the default was far too small, so I set it to 500 pixels. The result after doing this looks like the following:
Note that you will not be prompted for the line width when running the plugin a second time - you can change the line width with Image › Adjust › Line Width…
The two images composed are shown below:
