Where can I find data that used to be returned by allensdk.CellTypesCache.get_cells()

Question

Prior to allensdk version 0.14.5, the CellTypesCache.get_cells() function returned a large, nested structure containing information about cell morphology, ephys features, location, anatomical structure, tissue donors, etc. In version 0.14.5, the structure returned is flat and much smaller.

I see that some of this information is available through get_ephys_features() and get_morphology_features(), but I'm not sure where to find the rest. Where can I go to find out how to migrate my code to the new allensdk version?

Answer 1

Great question. We simplified the returned dictionary from CellTypesCache.get_cells for a few reasons:

1. There were a large number of fields that were variously: unexplained, not useful, distracting, and/or redundant with data returned from other functions.
2. The way brain structures were handled made it very difficult to filter cells by cortical layer across species.
3. The query involved a large number of joins and was fairly slow.

(2) was probably the most urgent issue we needed to address. The new dictionary structure is explained in a bit more detail here:

https://github.com/AllenInstitute/AllenSDK/wiki/Release-Notes-(0.14.5)

You are correct that you should look for ephys. and morphology features from CellTypesCache.get_ephys_features and CellTypesCache.get_morphology_features (or just CellTypesCache.get_all_features).

If there are any fields you were using in the old dictionary structure that are not now available in the current dictionary, let me know and we can find them again.