Error from Ryan [potential bug, tbd]

[neuroBazzi]

Hi Paolo,

Under the velasquez@salk.edu account at salk.metacell.us, the experiments Combined Populations 3 and Combined Populations 4 have the same input files but Combined Populations 3 has an error for the V2b cells.

For the section error, Rabies v3 has the error because there is only one slice in one of the sections while Rabies shifted fixed that by shifting the slices so that the lone slice moved into the next section (this experiment also seems to have the above problem with a neuron type having a seemingly random error). The source of this error appears to be cordmap.datal.utils.interpolate_atalas_section which assumes that the min and max value of z will be different.

@stephenlenzi email from Ryan about the error he mentioned yesterday during the call, when you have a chance could you please let us know what you think? cc @afonsobspinto

[stephenlenzi]

I will need to dig into this a bit deeper but I don't think this is a bug, but rather expected behaviour of the current implementation, which assumes full segments are provided. The position of a slice within a segment is adjusted to account for the overall size of the segment, which can vary.

For fiducial marker analysis this is implemented differently - here the client asked that we assume the sizes of the segments to be the same.

One solution would be to do something similar for typical cordmap, or provide the option.

[stephenlenzi]

am I right to assume this is running typical cordmap? the function mentioned is used by the normal cordmap pipeline but I dont think by the fiducial one

[neuroBazzi]

Thanks Stephen, I am not sure what function Ryan used. We can resume working on this with the new contract