Hi all, just thought I’d share some updates on the scanning and tiling code.
Example outputs can be found in this Youtube video, or at the Gigapans here, here and here.
348 images automatically captured, downloaded and tiled!
Cool pictures out the way, here’s the plan for anyone interested
The aim is to let a user put a sample under the microscope, set a background image, then leave the microscope running, finding its own path, until all of the interesting sample is scanned. Hopefully this will speed up a lot of medical uses with irregularly shaped samples.
To make this more useful (and to avoid issues with integrating Fiji or other tiling programs), our tiling code can copy all the images to the user’s computer in real time, and tile them based on the OpenFlexure metadata rather than filename. It estimates positions from the stage locations and camera stage mapping, finds better overlaps between each pair, then “shuffles” the images around to find the optimal position. Unlike in Fiji, you set your thresholds once all pairs have been processed, rather than at the start. This means the user can see the outputs and set thresholds accordingly, and quickly test multiple thresholds without rerunning the entire procedure.
This is still in early development, but if anyone has any suggestions, feedback or wants to test it out, please let me know.