Some cells are missing from output

I am trying to use CellTrek to map my single-cell RNA-seq data onto Visium ST coordinates. I have a dataset of 500k+ cells for my single-cell RNA-seq.

I ran the traint function with default arguments, and the co-embedding looks pretty reasonable. However, when I tried to run celltrek with the default arguments, I noticed that only a fraction of the cells in my single-cell dataset were mapped. I also tried downsampling my scRNA data to only map a portion with celltrek, but still there are a lot of cells missing from the output of celltrek. I am not sure why this is happening, but I am wondering what settings I should use in the celltrek function if I want to return coordinates for every input cell? Alternatively, if there are cells that have a low mapping to the ST dataset, and that's why they aren't showing up in the output, are there any metrics that celltrek returns to check the prediction condidence? Let me know if you need any more info to answer my question.

Thanks,
Sam

Start by reproducing the behavior with the traint and celltrek entry points, including the 500k-cell case and the downsampled input described in the report. Determine why output coordinates are missing, document the relevant settings or confidence metrics, and verify that the explanation matches the observed output.