Stitching SPIM artifacts

[matham]

We have LaVision light sheet data, where when stitched the overlapping areas have very visible artifacts.

The data set is 3 rows, 2 columns = 6 3D tiles (60GB). Below are examples of how the stitched images looks with various options. They all have the same issue.

After aligning with BigSticher I then fed the tiles coordinates to terastitcher and fused it there and it doesn't have any of these artifacts. And it doesn't seem to take much extra computations time. Alignment doesn't work great there so I'd prefer to be able to just use BigStitcher.

BigSticher

• With only smooth blending

  

• With no smooth blending

  

• With content based blending. It is super slow - just this one slice (out of 1,500) took 12 hours

  

• Next I tried using the intensity adjustment option. This is the adjustment preview

  

• Here's how it looks with intensity adjustment, 16bit, with smooth blending

  

• Here's how it looks with intensity adjustment, 32bit, with smooth blending

  

• Here's how it looks with intensity adjustment, 32bit, no smooth blending

  

TeraSticher

Here's how it looks with terastitcher with default options - no artifacts

The terasticher command was terastitcher.exe --merge --projin="locations.xml" --volout="..." --volout_plugin="TiledXY|3Dseries" --imout_format="tif" --algorithm=SINBLEND.

Any ideas what I can try to not have these artifacts?

[matham]

I think I see the cause of the issue. BigStitcher uses FusionTools.defaultBlendingRange to decide "how many pixels to compute the blending function on". The default (max?) value is 40, which is not enough when there is a lot of overlap and there's no way to set it from the GUI.

I changed that value to 950 (the precomputed cos array is upto 1000 so didn't want to get too close in case) and recompiled multiview-reconstruction-3.2.5.jar and substituted it in the plugins folder of fiji and it seems to have fixed the issue!

Here's how it looks in BigStitcher with `defaultBlendingRange` set to `950` - no artifacts

Here's the jar in case someone else needs it:
multiview-reconstruction-3.2.5.zip

Would it be possible to increase the defaultBlendingRange to like 2000 or more in the next release? There doesn't seem to a downside I think as it's just the max AFAICS.