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fixed typos
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calebweinreb committed Feb 5, 2024
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2 changes: 1 addition & 1 deletion docs/source/index.rst
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Expand Up @@ -20,7 +20,7 @@ Loading data is simple with the ``snub.io`` module. For example the following co
snub.io.create_project(project_directory, duration=1800)
snub.io.add_video(project_directory, 'path/to/my_video.avi', name='IR_camera')
snub.io.add_splikeplot(project_directory, 'my_ephys_data', spike_times, spike_labels)
snub.io.add_spikeplot(project_directory, 'my_ephys_data', spike_times, spike_labels)
We also support automatic conversion of NWB files to SNUB projects for a limited set of NWB neurodata types.
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2 changes: 1 addition & 1 deletion docs/source/tutorials.rst
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Expand Up @@ -10,7 +10,7 @@ Download the `example behavior and calcium imaging data <https://zenodo.org/reco
project generated in this tutorial is available `here <https://zenodo.org/records/10578025/files/miniscope_project.zip?download=1>`_.
This tutorial is based on head-mounted 1-photon calcium imaging and video recordings
from a mouse engaged in social interaction. The camera and microscope were synchronized
and have associated timestamps in seconds. There are also a behavior annotations
and have associated timestamps in seconds. There are also behavior annotations
for each frame generated by MoSeq.


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4 changes: 2 additions & 2 deletions paper.md
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Expand Up @@ -35,14 +35,14 @@ Direct inspection of behavior and neurophysiology recordings is hard because the

![Screenshot from SNUB.\label{fig:screenshot}](docs/media/screenshot.png)

We provide dedicated widgets and loading functions for exploring raw video, 3D animal pose, behavior annotations, electrophysiology recordings, and calcium imaging data - either as a raster or as a super-position of labeled regions of interest (ROIs). More broadly, SNUB can dislay any data that takes the form of a heatmap, scatter plot, video, or collection of named temporally-varying signals.
We provide dedicated widgets and loading functions for exploring raw video, 3D animal pose, behavior annotations, electrophysiology recordings, and calcium imaging data - either as a raster or as a super-position of labeled regions of interest (ROIs). More broadly, SNUB can display any data that takes the form of a heatmap, scatter plot, video, or collection of named temporally-varying signals.

In addition to the front-end GUI, we include a library of functions that ingest raw data and save it to a format that is readable by the SNUB viewer. The following code, for example, creates a project with paired electrophysiology and video data.

```
snub.io.create_project(project_directory, duration=1800)
snub.io.add_video(project_directory, 'path/to/my_video.avi', name='IR_camera')
snub.io.add_splikeplot(project_directory, 'my_ephys_data', spike_times, spike_labels)
snub.io.add_spikeplot(project_directory, 'my_ephys_data', spike_times, spike_labels)
```

We also provide a rudimentary tool for automatically generating SNUB datasets from Neurodata Without Borders (NWB) files, which contain raw and processed data from neuroscience recordings [@NWB]. The data in NWB files are stored hierarchically, and each component of the hierarchy has a specific neurodata type that reflects the measurement modality (e.g, "Units" for spike trains, "ImageSeries" for video). Our conversion tool generates a SNUB display element for each supported neurodata type. Users can optionally restrict this process to a subset of the NWB hierarchy (e.g., include pose tracking while excluding electrophysiology, or include just a subset of electrophysiology measurements).
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