Smart Imaging Macro Toolset for ACQUIFER Imaging Machine

This Fiji macro provides smart imaging (or feedback microscopy) tools for pre-scan/re-scan applications on the ACQUIFER Imaging Machine IM04. The macro will watch a directory reported by the IM04 to D:\IMAGING-DATA_GUI\JOBS\Image_Location.pth. Each generated image will be processed, a centring coordinate will be calculated and an Imaging Machine *.job file will be generated. These *.job files contain commands based on the ACQUIFER script language to modify the screening run.

The classical use case for this toolset is to identify a region of interest (ROI) in low resolution pre-screen data to subsequently centre and image it using higher magnification or multidimensional imaging parameters.

The macro currently provides access to the following SI functionalities.

• Template_Matching: Each pre-screen image is processed to detect the coordinates of an ROI that has the highest correlation to a given template (template.tif) image. Note: This macro requires to install the Multi Template Matching Fiji plugin (for installation instructions please see https://imagej.net/Multi-Template_Matching). For simplicity a pre-configured Fiji installation can be downloaded here: https://doi.org/10.5281/zenodo.2650855. For further detail please see: Thomas, Laurent SV, and Jochen Gehrig. "Multi-Template Matching: a versatile tool for object-localization in microscopy images." bioRxiv (2019): 619338 (https://www.biorxiv.org/content/10.1101/619338v1.)
• Center_Of_Mass: The coordinate of the centre of mass of the entire pre-screen image after thresholding is calculated. For a use case please see: Pandey, G.; Westhoff, J.H.; Schaefer, F.; Gehrig, J. A Smart Imaging Workflow for Organ-Specific Screening in a Cystic Kidney Zebrafish Disease Model. Int. J. Mol. Sci. 2019, 20, 1290( https://www.mdpi.com/1422-0067/20/6/129).
• Interactive_Clicktool: Each pre-screen image is opened and the user can interactively select a XY coordinate to be centred in the subsequent re-scan

Each functionality is represented as a Fiji macro function. This allows to readily expand the toolset with other image processing techniques.

The macro allows further to provide screening instructions based on the ACQUIFER script language that will be executed after automated centring of detected or selected XY coordinated.

The macro can be configured for smart imaging experiments that (i) execute scripts after a user-defined number of iterations (=well numbers) or (ii) execute scripts after a full loop run, i.e. all selected coordinates will be imaged in pre-screen mode before smart imaging jobs are executed

The current macro has been tested for IM software version 400.21. It will also work for other software versions (e.g. 500.xx) after minor modifications.