AllenSDK

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Filter pupil_width and other eye tracking columns similarly to pupil_area

5

Outlier removal and blink filtering was applied to `pupil_area`, `eye_area`, and `cr_area `in the `eye_tracking `attribute of the `BehaviorOphysExperiment `class, however a few additional columns were overlooked and should also...

matchings

It would be useful to have the `imaging_plane_group `and `imaging_plane_group_count `values that are currently available in the SDK dataset object `metadata `attribute also in the cache tables, including `ophys_experiment_table `and...

matchings

Omission times are logged incorrectly by 1 frame

13

**Describe the bug** The time assigned to omissions in the log is off by one frame. **To Reproduce & Expected Behavior** Compute flash-omission interval, i.e. the interval between the flash...

farznaj

mismatch in data types for `mouse_id` column for `from_s3_cache` vs `from_lims` methods

4

**Describe the bug** When retrieving the behavior session table from S3, the `mouse_id` column is int64. When retrieving the behavior session table from LIMS, the `mouse_id` column is a string....

dougollerenshaw

consistent naming of change column across tables

2

**Describe the bug** There is a column present in multiple tables in the Visual Behavior `behavior_ophys_experiment `class with a Boolean indicating whether a stimulus was a change or not, however...

matchings

**Describe the bug** Currently there is a metadata key called 'experiment_container_id' which should be 'ophys_container_id' to be consistent with the naming across the rest of the sdk **To Reproduce** ```...

DowntonCrabby

remove unecessary columns in stimulus_presentations attribute of BehaviorOphysSession and BehaviorSession

7

**Describe the bug** `BehaviorOphysSession `and `BehaviorSession `attribute `stimulus_presentations `currently has 2 unnecessary / uninformative columns - `image_set `and `index`. These should be removed. With allensdk rc/2.8.0 

matchings

standardize column name for auto reward across AllenSDK tables

2

AllenSDK returns tables with a column called either "auto_reward" or "autoreward" The science team would like to have a consistent name.  **Describe the solution you'd like** I'd like the...

DowntonCrabby

Run learning-mFish data through the full LIMS queues.

1

Marina is happy with the segmentations, traces and nway matching and is asking the data to be fully processed not just the single container already completed. She sent over a...

morriscb

VB cells table has more experiments than experiments table

2

AllenSDK 2.12.4 Checking the number of experiments in the `ophys_cells_table `and the `ophys_experiment_table `using` .from_S3_cache` gives a different number of experiments  Not sure why this is the case! Happy...

matchings