Hi Everyone,
I'm new to FIJI and am hoping to troubleshoot the Stitching plugin. I was using the plugin for 10X images of neurospheres and ran into issues with alignment. I took images in a snake pattern with a lot of overlap (>50%). I then used the "unknown position" option for the Grid/Collection stitching; Grid: snake by rows did not do as good a job. The result is mostly accurate, but parts of the fused image (e.g. the Hoechst channel) shows a double-vision problem; e.g. the same nuclei in two photos are shown next to each other instead of aligned and merged on top of each other.
I've set up a dropbox account, created a shared folder, and sent an invitation to the list. If it the image opens successfully, the double-vision nuclei are in the upper right of the neurosphere pictured. The link is:
https://www.dropbox.com/home/FIJI%20PictAre there any settings I can adjust? I've tried increasing the regression threshold to 0.7 but it did not help. Also, there is a note in the cookbook about registering different channels using hyperstacks, but I'm having a bit of trouble following through with it.
"However, if you want to do that anyways simply convert channels into time-points and run it as if it was time-lapse registration. Afterwards you can convert it back. The easiest to achieve this is to use Image -> Hyperstacks -> Re-order hyperstack ..."
Any suggestions or directions for converting channels to timepoints would be appreciated.
Thank you for your help.
Sincerely,
Cheuk
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