search

LidkeLab / smite

Single Molecule Imaging Toolbox Extraordinaire
MIT License
15 stars 3 forks source link

Pixel conventions #19

Open dschodt opened 2 years ago

dschodt commented 2 years ago

Some core pieces of smite are using the pixel convention that the center of a pixel is coordinate 0.5. As in, if we have a one pixel image, the left edge is coordinate 0 and the right edge is coordinate 1. We had previously discussed using the convention that the center of a pixel is the index (i.e., left edge is coordinate 0.5 and right edge is coordinate 1.5). Do we still plan to make this switch? If so, what needs to be changed?

From what I've seen, changes will be needed in:

kalidke commented 2 years ago

Do SimSPT and SPT use GaussBlobs or their own generators? Everything should use gaussblobs.

dschodt commented 2 years ago

SimSPT only generates trajectories, but the trajectories get restricted to the frame size using the pixel convention (i.e., a frame size of 1 pixel restricts trajectory coordinates to [0, 1] instead of [0.5, 1.5]). SimSMLM seems to work the same way.

smi.SPT (and several other classes) use the pixel convention to convert from localization coordinates to image indices.