Preventing Tile Migration when using the Grid/Collection Stitching Plugin

Hello all,

I’m currently using the Grid/Collection Stitching Plugin to stitch together wells from 6-well plates.

The majority of the time, the stitched images look decent. However, the output sometimes (20-30% of the time) looks like this:

The problem is the black squares at the center of the well. Seems like the corner tiles of the image are being moved to the center by the algorithm to ensure a “better fit” (which is detrimental in this case).

I have tried playing with some parameters to prevent tile migration and the only reasonable solution has been to set the regression threshold extremely low (0.001) and the avg/max displacement thresholds very high (10,000). Even with these parameters, I sometimes see failures.

For reference, here are the current parameters fed into the GCS Plugin:

  • Fusion method: linear blending, regression threshold: 0.001, max/avg displacement threshold: 10000, absolute displacement threshold: 10000, “compute overlap”, “save computation time (but use more RAM)”, image output: “fuse & display”

Any ideas on why this might be happening and how it can prevented/resolved?


Hi @Bhaskar_Yechuri

Sorry it took so long to get an answer.

If you haven’t tried big stitcher, I’d really recommend it

It’s from the same authors of the plug-in you used, but with extra tools to quickly visualize the results and fix mistakes by hand if needed .

Good luck

Hey John,

Thanks for the suggestion. I started looking around for other stitching plugins based on your message and found MIST, which stitched my images better than Grid/Collection Stitching.

I guess it isn’t a direct solution to the problem, but since switching over, I haven’t had any stitching issues.