Stitching Images Acquired in Micro-Manager
There are a number of programs available for stitching images acquired in Micro-Manager, or stitching images more generally. For images acquired from Micro-Manager, the simplest option is to use the Grid/Collection Stitching Plugin. This is installed by default in the Fiji distribution. The major disadvantage to this program is that it will not stitch images larger than 2.14 gigapixels.
Acquiring a grid of images in Micro-Manager
The easiest way to do this is by using the Create Grid option in the Multi-Dimensional acquisition GUI. To access it:
- Open up Multi-Dimensional Acquisition in Micro-Manager.
- Click the Edit position list button.
- Click the Create Grid button.
- Move to the left edge of your sample and click the left-most set button.
- Repeat this procedure for the other three edges of your sample.
- Set the overlap (5-20% seems to work well).
- Acquire your data (make sure to save in Image stack format).
- You may want to use the BFcorrector plugin to flat-field correct your images.
Stitching images using the Grid/Collection Stitching plugin in Fiji
- The Grid/Collection Stitching Plugin is located in Plugins -> Stitching -> Grid/Collection Stitching.
- In the first dialog box, select Type: “Positions from file” and Order: “Defined by image metadata”
- In the second dialog box select the first position in your grid for “Multi series file”.
- Depending on the orientation of your camera relative to your stage you may need to select “Invert X Coordinates” or “Invert Y Coordinates”.
- Otherwise, the default options usually work well.
- Hit OK, and you should have your stitched image in a few minutes.
- This works for single channel and multicolor images, and should work for Z-stacks as well, although I haven’t tested it as extensively for Z-stacks.
Information about other stitching options is available on the NIC wiki.