Hi Terastitcher developers,
We're currently employing an in-house developed napari plugin to generate an XML file (xml_import.xml) for importing our dataset into the GUI version of Terastitcher, and we are experiencing duplication effects in the stitched images depending on the import file.
Dataset Details
COLM lightsheet microscope generated (similar to Raju Tomer’s model)
Each dataset consists of 421 planes (z-stack)
Each plane comprises a 4x1 matrix of tiles (rows,columns), single-channel
Camera: Orca Flash V4 with frame size: 2048x2048px
16-bit images
The plugin reads the vertical tile overlap (38.8%) from our configuration file Experiment.ini to determine mechanical displacements in xmlimport.xml. This overlap gives a vertical mechanical displacement of 1252 (i.e., 2048*(1-overlap)). However, this value results in duplication of features in the stitched image, as shown below.
As a workaround, we manually adjusted the mechanical displacements in the import XML to 6000 (with pixel size 5um instead of 1um),_ leading to respective ABS_V values of 1200, 2400, and 3600 for each tile. This adjustment not only resolves the duplication problem but also changes the frame size to 2048x5648 (compared to the original 2048x5804). From this, we suspect a potential issue with the merging process when using precise overlap calculations. We are trying to understand why this is happening so we can adapt the plugin, and would appreciate any insights or suggestions.
Many thanks!
Yoseline
Hi Terastitcher developers, We're currently employing an in-house developed napari plugin to generate an XML file (xml_import.xml) for importing our dataset into the GUI version of Terastitcher, and we are experiencing duplication effects in the stitched images depending on the import file.
Dataset Details
The plugin reads the vertical tile overlap (38.8%) from our configuration file Experiment.ini to determine mechanical displacements in xmlimport.xml. This overlap gives a vertical mechanical displacement of 1252 (i.e., 2048*(1-overlap)). However, this value results in duplication of features in the stitched image, as shown below. As a workaround, we manually adjusted the mechanical displacements in the import XML to 6000 (with pixel size 5um instead of 1um),_ leading to respective ABS_V values of 1200, 2400, and 3600 for each tile. This adjustment not only resolves the duplication problem but also changes the frame size to 2048x5648 (compared to the original 2048x5804). From this, we suspect a potential issue with the merging process when using precise overlap calculations. We are trying to understand why this is happening so we can adapt the plugin, and would appreciate any insights or suggestions. Many thanks! Yoseline