CODEWITHSUNDEEP
allen-sdk
Luke
Luke

Reputation: 11644

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

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?

Upvotes: 0

Views: 53

Answers (1)

davidf
davidf

Reputation: 313

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.

Upvotes: 1

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