python-neo

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Error in reading NWB files

4

Tried with two sample files: 1) https://object.cscs.ch/v1/AUTH_c0a333ecf7c045809321ce9d9ecdfdea/VF_paper_demo/live_paper/temp/525011725_ephys.nwb 2) https://celltypes.brain-map.org/api/v2/well_known_file_download/742807112 Installed Neo using the master branch (June 22: [commit](https://github.com/NeuralEnsemble/python-neo/commit/13d3fe312a87913d944886d808eb013cab2c5dcf)) and tried the following using Python 3.8: ```python from neo.io import NWBIO...

appukuttan-shailesh

Add validation to NWBIO.write()

1

As a quality control step, we should run the [pynwb validator](https://pynwb.readthedocs.io/en/stable/validation.html) when writing an NWB file with NWBIO. Since this might be slow, we might need to make this optional...

apdavison

Add an error message suggesting to convert to a later NWB format

1

Should fix #1131

legouee

The #949 do not implement this. It must implemented outsside.

samuelgarcia

copy behaviour of annotations and object identity

3

Annotations of objects are by default not deepcopied when manipulating an object, e.g. upon slicing of a signal. However, array annotations are explicitly deepcopied (see https://github.com/NeuralEnsemble/python-neo/issues/809#issuecomment-619902320), whereas this is not...

JuliaSprenger

Annotation handling when grouping signals

9

This is a follow up of #625. When loading information using the rawio framework, annotations are handled differently depending on the grouping modes of the signals. When splitting signal into...

JuliaSprenger

improves blackrock spikes in nev

3

Hi, I tried to open a .nev file (2.3 version) and I found t2o bugs and fix them: -The timestamps gives one element less that the amount of spikes. I...

ferchaure

2D array_annotations for ImageSequence objects

3

As already touched upon in issue #745 , one step towards better representing geometries and spatial information of data is to have array_annotations which are of the same dimensionality as...

rgutzen

Block.filter and Segment.filter should do use "OR" but "AND" by default

2

@JuliaSprenger @mdenker @Kleinjohann Block.filter and Segment.filter should do use "OR" but "AND" by default. It is more natural when you do a query to have a list of condition linked...

samuelgarcia

Option to copy array annotations in `duplicate_with_new_data()` function

2

In the general case, it's desirable to not copy array annotations when duplicating an object with new data. However, sometimes it may make sense, e.g., when z-scoring an analog signal....

mdenker