diff --git a/docs/source/index.rst b/docs/source/index.rst index dd713f1..ce27546 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -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. diff --git a/docs/source/tutorials.rst b/docs/source/tutorials.rst index be35657..33a9c68 100644 --- a/docs/source/tutorials.rst +++ b/docs/source/tutorials.rst @@ -10,7 +10,7 @@ Download the `example behavior and calcium imaging data `_. 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. diff --git a/paper.md b/paper.md index 0295580..e57c4cb 100644 --- a/paper.md +++ b/paper.md @@ -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).