To install:

• Create and activate a virtual environment, e.g.

  conda create -n rotate2d python pip
  conda activate rotate2d

• Clone rotate2d and PIP install it, e.g.

  git clone https://github.com/chunglabmit/rotate2d
  pip install ./rotate2d  

To run:

rotate2d

To use:

From the menu, select File -> Open Fixed and pick a ZARR directory, select File -> Open Moving and pick a ZARR directory. Hit the button marked "Center" to set the center for rotation, then hit the button marked "Show" to show the fixed image in red and the moving image in green.

You may have to select the z slice for each using the z-height controls and for large images, set "Downsample" to 2 or more to reduce the display image size. After any change, hit "Show" to redisplay.

You should adjust the offsets and angle until the images align. Then select File -> Save from the menu. This will let you save the rotation and translation parameters as a JSON file.