This plugin is designed to simplify the process of acquiring tiled images from multiple regions (e.g. multiple brain sections) on a slide. It allows you to specify multiple regions to acquire, after which you can start the acquisition and Micro-manager will automatically acquire a set of tiles covering each region you specify. This way you can walk away from the microscope while it does the time-consuming acquisition. The images can then be stitched using the Grid/Collection stitching plugin in Fiji.
To use it, you first specify a directory and filename to save the images to. Then focus on part of your section and press the “Add Point to Current Region” button. Each time you press this button, it will remember the current point as part of the current region. The area acquired will be the rectangle which contains all points that have been added (the bounding box). Once you have added enough points to define the extents of the region, press “Save Region for Acquisition” and the region will be saved for later acquisition. You can then define another region as above. Once all regions have been defined, press “Acquire All Regions” and Micro-manager will move from region to region, acquiring a tiling set of images that covers each region.