Pixel-wise decoding for Polaris

[elaubsch]

This PR introduces an algorithmic change to Polaris that increases the number of pixels sent through the SpotDecoding application. Previously, we performed peak finding to determine which pixels were decoded. Now with this change, we will threshold the spot probability image and decode all pixels above a certain spot probability. Then, we create a mask for all of the pixels decoded to genes and apply this mask to the spot probability image. We then perform peak finding on this masked image to call the gene locations. This change is like a compromise between Polaris' original method and pixel-wise decoding methods that are common in MERFISH analysis pipelines. We found that this method increases the number of spots decoded to genes by Polaris, while yielding results with a better correlation to bulk sequencing data.

This change redefines of the threshold parameter for the predict method. Instead of being used in peak finding, this parameter is used to create a mask for tissue area. Therefore, the default value has been changed.

This PR also includes changes the output of Polaris that are unrelated to the algorithmic change. Polaris previously returned df_spots and df_intensities, but now these two outputs have been concatenated column-wise to yield a single DataFrame.