If you haven’t changed anything from the Tile Creator, the names of the files should be in this format: img_n_MMStack_n-Pos_.ome.tif.įigure 11: The grid stitching window with all the options. The ‘Files names for tiles’ should contain the general name for the files you created. Then select the directory that you stored the files in. The ‘Tile overlap’ is normally fine at 20%, but you may need to change some numbers in order to get the desired image.Ĭhange the ‘First file index x’ and ‘First file index y’ to 0. In the following window, input both ‘grid size x’ and ‘grid size y’. The files created by Micro-Manager have a specific setting that shows x, y and z positions when acquired.įigure 10: Grid/Collection stitching window. In the Grid/Collection stitching window, select ‘Type -> Filename defined position’. Using FIJI (if you are using ImageJ you probably need to download the plugin for this), go to 'Plugins -> Stitching -> Grid/Collection stitching'. The stage moves to the calculated positions and images are stored at each position of the list.įigure 9: List of positions of the stage for imaging. In the ‘Multi-Dimensional Acquisition’ window click ‘Acquire’. Move the stage to the bottom right corner of the area to be imaged and click on the bottom and right hand ‘Set’ buttons.Īlternatively, you could set up the view you are at as the centre, and Micro-Manager will take another 8 pictures surrounding that centre (in a 3x3 frame).Ī list of calculated positions will appear in the stage position list (Figure 9). Move the stage (using the PatchPad or Control Cube) to the top left corner of the area to be imaged and click on the upper and left hand ‘Set’ buttons. Overlap can be set as a percentage - 10-20% normally works well. Click on ‘Create Grid’ to open Tile Creator (Figure 8).Įnter the pixel size as determined above in ‘Calibrating Micro-Manager Tile Creator’. You will see a blank list on a window called ‘Stage Position List’. Under 'Multiple positions (XY)', click on ‘Edit position list…’. The other option is not particularly useful if you are taking a lot of images or require faster acquisition.įigure 7: Selecting Acquisition Order and Multiple positions in the Multi-Dimensional Acquisition window. For simplicity, select the ‘Save format: Image stack file’ option. Images are saved to the disk in the ‘Directory root’ set up under ‘Save images’ in the Multi-Dimensional Acquisition window. The position is the important one at the moment. You will have different ‘Acquisition order’ options. If you have more than one channel and more than one time point to record, you should check ‘Time points’ and ‘Channels’. In Micro-Manager, select 'Multi-Dimensional Acquisition' (Figure 7). Warning if you are using LinLab2: it cannot be operated at the same time as Micro-Manager in this configuration, because the control of COM ports cannot be shared. Micro-manager has an extensive list of devices they support. You can always add another device in a similar way during this stage, such as cameras and shutters. This is the configuration file that should be loaded on startup of Micro-Manager to use this software to control the XY stage. In the following window, click on 'Undefined' and enter the COM port number identified above from the drop-down list that appears, then click ‘OK’ (Figure 3).įigure 3: Adding the COM port you found out for the XY stage.Ĭlick on ‘Next’ through the following sequence of windows and follow on-screen instructions to finally save this new configuration file. In the Micro-Manager software, select 'Tools' and then 'Configuration Wizard' (Figure 2).įigure 2: Hardware configuration Wizard for Micro-Manager.Īdd the XY stage. Figure 1: Finding out which COM port belongs to the XY stage. You can find which COM port belongs to the stage by unplugging the USB cable of the stage controller, making a note of which COM port disappeared, then plugging it in again to double-check. To check this, open Windows Device Manager and check under ports (COM & LPT), (see figure 1). The COM port number of the motion control card driving the XY stage is required for this. Acquiring a series of images and stitching them together using FIJI Setting up the Micro-Manager configuration fileįunctions in Micro-Manager that have control of the XY stage will require this to be added to the configuration file in use.
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