Leginon

Hi everyone,

We are using the MSI Raster application and we would like to automatically target the center of squares from the square targeting mode, so that the user would just have to (de)select squares they are (not) interested in (because they are damaged) and we can lay the same grid over all the squares in Subsquare targeting to acquire the whole square (see image Subsquare_Targeting.png for an example). Eventually, the system should acquire a low-mag (e.g. ~ 3000x) overview of the whole square, which will be processed further.

Currently, we can manually set a targets in the Square Targeting node. To automate the process, we would like to be able to automatically detect the squares in the grid image and target their centers.
When the grid atlas is acquired, the square targeting node puts together the atlas together into a mosaic. The «Find Squares» button in the toolbar of the square targeting node is not doing anything (no squares are found and no log messages are produced). Are there settings we would need to adjust for this function to work? Or is it not implemented yet? I saw some square targeting code in the source code, but can’t figure out how it’s linked to this button.
Also, I looked at square centering in the MSI-RCT raster (3.0) application. I’m not sure if this could be adapted to our purpose to automatically center squares (e.g. the user selects the square approximately, Leginon centers on this squares and proceeds from there). Currently, the "Centered_Square" node always fails with "Process target failed: ‘NoneType’ object in unsubscriptable" when I manually give an acquisition target in the middle of the square.

What approach would you recommend to automatically target the center of the squares? How can we adapt the settings or insert our own targeting scripts to automatically target the centers of all squares?

Attached is a grid atlas image on which the squares should be detected and targeted (as tif and .mrc).

Best,
Joel