I would like, within a script, to read traces previously generated from Simple Neurite Tracer and store them as ROIs for post-tracing analysis. However, the coordinates of the ROIs generated using “File > Import > Tracings” (from Neuroanatomy site) are different from those in the .swc files. I am attaching a simplified example where the .swc trace is properly overlaid on the image when loaded from the SNT interface but not when imported, e.g. with something like
run("Tracings (Traces/(e)SWC)...", "open=C:\\trace.swc apply_spatial voxel_width=1 voxel_height=1 voxel_depth=1 unit=pixel x_offset=0 y_offset=0 z_offset=0 x_scale=1 y_scale=1 z_scale=1 render=[2D ROIs (stored in ROI Manager)]");
What am I missing? Suggestions on how to accomplish this task?
== test image ==
== results from load in SNT and import ==
== trace.swc ==
# Exported from "Simple Neurite Tracer" version 3.1.4 on 2017-06-27T11:13:02.111 # https://imagej.net/Simple_Neurite_Tracer # # All positions and radii in pixels # WARNING: Usage of pixel coordinates does not respect the SWC specification # 1 0 186.0 55.0 0.0 0.0 -1 3 0 63.0 191.0 0.0 0.0 1