SI Coordinate Systems

Introduced in ScanImage 2022.1.0, the a coordinate systems page was introduced to organize alignment data into multiple coordinate system data files. If there are commonly made changes made to the microscope that affect alignment, then the SI Coordinate Systems page can help associate alignment information for each configuration.


The most common example for its use would be in the case of switching between objectives. For each objective, a different stage-scanner alignment must be conducted to reestablish the proper relation between scanned optical degrees and microns distance between pixels. In this case one would

  1. Do a stage-scanner alignment for one objective (and any other alignments). Alignment data is saved to the currently applied coordinate systems data file when the Generate Alignment button is clicked.

../_images/Stage-Alignment.png ../_images/Scanner-Scanner+Alignment+saving.png
  1. Swap objectives.

  1. Visit the SI Coordinate System configuration page.

  1. Create a new coordinate system file for the next objective (can name the files according to the objective).

  1. Select the newly created system file and click Apply to change the currently applied coordinate systems data to the selected one.

  1. To rename the file that has the stage-scanner alignment data, double click it in the table.


You cannot edit the currently loaded coordinate system file name. To edit a file name (from ScanImage), you must select and apply another coordinate system file.

  1. Do a second stage-scanner alignment with the new objective and new coordinate system file. Each alignment is intact in its own separate file

To revise or edit the alignment data in a file, just do the alignments again and click the Generate Alignment or Save Scanner Alignment Transform buttons to overwrite the file with the entire current state of the ScanImage alignment (including stage, scanner, camera, stimulation, SLM alignments).


Alignment data is stored within a CoordinateSystems folder located in the ‘Machine Data File name’.ConfigData folder that is stored in the same directory as the machine data file. They contain a struct which contains the affine transformation matrices and relations to other coordinate systems that make up the Coordinate system configuration.