Roberto

brainGridData.npy

1

Hi, Can you give me some insights in how you creaed the brainGridData.npy file? Thanks!

Broken .get_performance_metrics() method in VisualBehaviorNeuropixelsProjectCache.from_s3_cache(cache_dir=neuropixel_dataset_behavior)

2

**Describe the bug** .get_performance_metrics() will lead to ``` --------------------------------------------------------------------------- KeyError Traceback (most recent call last) File /alzheimer/Roberto/Software/mambaforge/envs/De-Filippo-et-al-2023/lib/python3.9/site-packages/pandas/core/indexes/base.py:3652, in Index.get_loc(self, key) 3651 try: -> 3652 return self._engine.get_loc(casted_key) 3653 except KeyError as...

Hi, s1 and s2 variables missing, definition taken from https://github.com/MouseLand/stringer-pachitariu-et-al-2018a/blob/8dce0d516bb8a4b16e245b897403d76cd1d25ae7/multiDactivity/SVCA.m#L24 Relative to issue #1

File missing field

2

Hi, No field "motionSVD_stim" is present in stimspont mat files. So an error is raised on this line: https://github.com/MouseLand/stringer-pachitariu-et-al-2018a/blob/8dce0d516bb8a4b16e245b897403d76cd1d25ae7/stimspont/sharedVariance.m#L96

s1 variable missing in peerPC_cov.m

1

Hi! Thanks for making all the code available. I have a problem using peerPC_cov.m, where is the s1 variable from? I tried the second output of svdecon but it doesn't...

add columns to unit table in plot_sorting_summary

1

Hi, I don´t understand how to add some data to the unit_table showed in plot_sorting_summary. I see that the `unit_table_properties` arg should do that, but how to use it? The...

read_spikegadgets broken for neuropixel recordings

15

Hi, The read_spikegadgets from spikeinterface was working with neuropixel probes with this committ 83a84b2 but now it is broken. ``` File "C:\Users\SciencePerson\miniforge3\envs\spikesorting\lib\site-packages\IPython\core\interactiveshell.py", line 3550, in run_code exec(code_obj, self.user_global_ns, self.user_ns) File...

error when importing spikegadget .rec file with multiple NPX 1.0 probes

2

https://github.com/NeuralEnsemble/python-neo/issues/1548#issue-2512404132

# Overview: rf_mapping.get_receptive_field fails with following error: ``` File /alzheimer/Roberto/Software/mambaforge/envs/Visual_decoding/lib/python3.11/site-packages/allensdk/brain_observatory/ecephys/ecephys_session_api/ecephys_nwb_session_api.py:95, in EcephysNwbSessionApi.get_stimulus_presentations(self) 93 print("wvfdvwcw") 94 rgb_color_match = table["color"].str.match(color_triplet_re)#.astype(bool) ---> 95 table.loc[rgb_color_match, "color_triplet"] = table.loc[ 96 rgb_color_match, "color"] 97 table.loc[rgb_color_match, "color"]...

Improve memory management in clustering_qr.kmeans_plusplus

13

This modification avoids the creation or immediately deletes unnecessary tensors in clustering_qr.kmeans_plusplus. It helps with OOM errors (#746 ) happening at https://github.com/MouseLand/Kilosort/blob/b2f5ded41aaa7e13ed44bf43ecf488770ef54753/kilosort/clustering_qr.py#L202 Xg can at sometimes be quite big (5GB...