In the alignment process, you have various options to align image data. Note that you can change the alignment mode during the alignment process. The alignment edits you have made are preserved, but you have to restart the pinning process if you have inserted any pins before changing the mode.

Note that the alignment process can be executed multiple times. Each time you run the alignment process, the end result of the last alignment is used as the starting point for the new alignment. If the initial image was far out of alignment at the start, it is easiest to do the alignment process once roughly, and then do the alignment process a second time with more precision. The second alignment will use the first alignment as a starting point, and will allow you to establish a more precise alignment quickly.

  1. You have loaded a ZEN Connect project and activated the alignment process.
  1. In the Alignment toolbar, select one of the following alignment modes, and select the region you want to align.

Translate Only

  1. Click and drag with the mouse to translate the image you are aligning with respect to everything else.
  2. You can zoom in and out with the mouse wheel, or press and hold the Ctrl key to pan while you are in the process of aligning the image.

Translate and Rotate Only

  1. Right-click at the location you have lined up to insert the first pin, a red and grey pin icon. The pin locks the image to the reference at this location. Press DEL to remove the last pin you inserted.
  2. After you insert the first pin, your input will rotate the item around the first pin, when dragging it with the mouse.

Translate, Rotate and Scale Only

  1. If one of the images is smaller than the other, you can scale it. Right-click to insert a pin.

  2. Drag with the mouse to scale and rotate the image.

Translate, Rotate, Scale and Shear

  1. Right-click to insert a second pin, and drag with the mouse to shear the image.
  2. After you insert the second pin, your input will also stretch and shear the item.

Image data from microscopes should not need to be stretched or sheared to perform alignment. If you need to provide much input after inserting the second pin, this might be an indication of other problems, such as equipment calibration issues.

Alignment Handles

  1. If you select Alignment Handles, you can use handles to rotate, translate, and scale the image.

Flipping the image horizontally and vertically

You can flip your image, to mirror it.

  1. To flip the image horizontally, click .
  2. To flip the image vertically, click .

Reset alignment

  1. To reset the alignment you performed, click .
  2. The alignment is reverted as it was when you started aligning. The Alignment mode ist still activated.

Cancel alignment

  1. To cancel the alignment you performed, click .
  2. The current alignment is cancelled and reverted to the alignment in place before you started the Alignment Mode. The alignment mode is not activated any longer.

Finish alignment

  1. Click Apply to finish the alignment mode and to apply the alignment information.