Dear all,
I often record large tile scans, also in z dimension using a LSM710 microscope and the Zen software v2.3. While after recording all unstitched images look usually fine, I sometimes get errors after stitching, mostly in the channels of the 514nm laser. I think it is a software problem though since unstitched it looks fine and overlap between the tiles is high. Does anyone could give me an advice how to solve this? I need the pictures stitched since I want to do 3D reconstructions using Imaris software.
Sorry, image quality of attached pictures a bit lousy.
Best wishes,
Urs
I think you need to have a bug worked out in the software. If you have stitching capability, there shouldn't be an issue (I know the stitching add-on isn' included in an initial setup). You may need to save your file two ways to do what you want (3-D constructions and stitching). [1]Save your Z-stack (for 3-d capabilities) and [2] Process your z-stack as a maximum intensity projection (MIP) and then apply the stitch. If you stitch before the MIP you will likely have issues. If this doesn't work, I recommend contacting your Zeiss rep about the issue. I hope this helps!
Elliot
Hi Urs,
I also use the same confocal as you and actually I have no problem reconstructing the tiles - but I have a problem in the time that it takes for large datasets (the computer has not much RAM). Therefore, I use the Fiji plugin to stitch my microscopy data and it works very well. You just need to have your microscopy raw data (.lsm) and the Fiji plugin works just with that file. To learn how to work with the plugin is straight forward.
In the microscope, I use an overlap of 10% for acquisition and for the online stitching I use a threshold of 75%. I never had problems in the online stitching.
I hope this is helpful!
- Badges
- Science topic
- Similar topics
- Cognitive Science
- Thinking