Multi-angle images fusion

Hereafter, we illustrate how to perform multi-angle images fusion using the CLI with the provided test dataset named p58.

Manual initialisation

When the “angles” (rotations around axis) between observations is important and not known precisely it is recommended to perform a manual initialisation to help the fusion registration.

From the timagetk root directory:

multiangle_initialisation data/p58/p58.json

You should get a new dataset named multiangle_landmarks with the landmarks files (p58_t*_floating_ldmk-**.txt) and some snapshots generated by the program.

For example, with the first time point (t0) of p58, for the first two ‘views’ (top and tilt1), you should get something like this:

This interface has 3 main panels:

  • the top-left panel show you a top view intensity projection of the image that will later be used as “reference image” during the fusion

  • the top-right panel show you a top view intensity projection of the image that will later be used as “floating image” during the fusion

  • the lower panel show you 5 slices with the obtained the rigid transformation using the points you placed on the top panels. This panel is not interactive, but will be automatically updated every time you place a point (starting after a minimum of 3 points). The colors are as follows:

    • in red, you have the reference image (the one in the left panel)

    • in green, you have the rigid transformed floating image using the transformation defined by the landmarks

    • in blue, you have the rigid transformed floating image using an automatic rigid registration initialized by the landmarks transformation

With this interface, you can perform the following actions:

  • press r to rotate the image on the right panel

  • press a and left-click on a panel to add a point on both side

  • left-click (and maintain) on a colored point to drag it around

  • press q or close the window to move on to the next iteration (if any)

  • press u to update the lower panel (should be done automatically when adding a new point)

Fusion

From the timagetk root directory:

multiangle_fusion data/p58/p58.json --manual_init

Important

Here we used the option --manual_init as we proceeded to manual initialization of the transformation by placing landmarks!

You should get a new dataset named fusion with the fused images (p58_t*_fused.tif) and some snapshots generated by the program.

For example, with the first time point (t0) of p58, you should get something like this: