NeuraLib2
Packages
Atlas
BrainRender
Region Reconstruction
ROI Reconstruction
Probe Reconstruction
ROI DataFrame
RoiClassifierDataFrame
RoiNormalizedDataFrame
RoiSubregionDataFrame
CellAtlas Dataframe
Example of loading the dataframe
Structure Tree
Slice View
Basic Usage
Angle Offset
Region Annotation
Max Projection
Example notebook
neuralib.atlas
Example of ML offset in coronal slice
Example of DV offset in sagittal slice
Example of Annotate regions
Example of Annotate regions in transverse view
Example of max projection
Imaging
Spikes
OASIS
Cascade
WideField
Sequence Preprocessing
Widefield Transform
FFT View with Bokeh
Align with Napari
Example notebook
neuralib.imaging
Load Suite2p results
See the Suite2p registered ROIs
Calculate dF/F
Calculate deconvolution spikes using OASIS method
Predict spikes from dF/F using pre-trained model from Cascade
Parser
Cellpose
StarDist
Suite2p
Facemap
DeepLabCut
ScanBox
Metadata information
Metadata to Json
Screen Shot file to tiff
ScanBox Imaging View
Confocal Scan
LSM Data
CZI Data
Morphology
SWC Data
Metric
Position Decoding
place_bayes
RasterMap
Supported Input Data
Example notebook
neuralib.model.rastermap
Example of cellular dataset
Example of widefield imaging dataset
Utility
General Plotting
Image library
Array Factory
CV2 Labeller
IO processing
Helper Function
Example data
Persistence Class
Define a Persistence Class
Cooperate with PersistenceOptions
Dynamically Generated Methods
Auto-Increment Field
Pickle Format
Utility Tool
Google SpreadSheet
Slack Notification
Bokeh Base Module
Simple Example
General Application Structure
Example notebook
neuralib.plot
Plot the data with violin and box with dots
See correlation and histogram of two variables
Diagonal plot value comparison
Dotsplot with colormap
Venn Diagram
Grid subplots
Reference
neuralib
neuralib.atlas
neuralib.atlas.brainrender
neuralib.atlas.ccf
neuralib.atlas.cellatlas
neuralib.atlas.data
neuralib.atlas.map
neuralib.atlas.plot
neuralib.atlas.typing
neuralib.atlas.util
neuralib.atlas.view
neuralib.cellpose
neuralib.cellpose.core
neuralib.dashboard
neuralib.dashboard.base
neuralib.dashboard.examples
neuralib.dashboard.tool
neuralib.dashboard.util
neuralib.dashboard.view_brain
neuralib.decoding
neuralib.decoding.position
neuralib.deeplabcut
neuralib.deeplabcut.core
neuralib.facemap
neuralib.facemap.core
neuralib.facemap.plot
neuralib.imglib
neuralib.imglib.array
neuralib.imglib.color
neuralib.imglib.io
neuralib.imglib.labeller
neuralib.imglib.norm
neuralib.imglib.transform
neuralib.io
neuralib.io.core
neuralib.io.csv_header
neuralib.io.dataset
neuralib.io.json
neuralib.io.output
neuralib.io.pyh5
neuralib.locomotion
Locomotion
neuralib.locomotion.epoch
neuralib.locomotion.position
neuralib.locomotion.spatial
neuralib.morpho
neuralib.morpho.swc
neuralib.persistence
neuralib.persistence.cli_persistence
neuralib.persistence.persistence
neuralib.persistence.validator
neuralib.plot
neuralib.plot.colormap
neuralib.plot.figure
neuralib.plot.plot
neuralib.plot.psth
neuralib.plot.tools
neuralib.plot.venn
neuralib.rastermap
neuralib.rastermap.core
neuralib.rastermap.plot
neuralib.rastermap.run
neuralib.registration
neuralib.registration.coordinates
neuralib.scan
neuralib.scan.core
neuralib.scan.czi
neuralib.scan.lsm
neuralib.scanbox
neuralib.scanbox.core
neuralib.scanbox.view
neuralib.spikes
neuralib.spikes.cascade
neuralib.spikes.oasis
neuralib.stardist
neuralib.stardist.base
neuralib.stardist.core
neuralib.stardist.run_2d
neuralib.suite2p
neuralib.suite2p.core
neuralib.suite2p.plot
neuralib.suite2p.signals
neuralib.tools
neuralib.tools.gspread
neuralib.tools.slack_bot
neuralib.typing
neuralib.typing.alias
neuralib.typing.func
neuralib.util
neuralib.util.dataframe
neuralib.util.deprecation
neuralib.util.func
neuralib.util.gpu
neuralib.util.interp
neuralib.util.logging
neuralib.util.profile
neuralib.util.segments
neuralib.util.table
neuralib.util.tqdm
neuralib.util.unstable
neuralib.util.utils
neuralib.util.verbose
neuralib.widefield
neuralib.widefield.align
neuralib.widefield.ccf
neuralib.widefield.data
neuralib.widefield.fft
neuralib.widefield.fft_view
neuralib.widefield.preproc
neuralib.widefield.svd
neuralib.widefield.transform
NeuraLib2
neuralib
neuralib.atlas
neuralib.atlas.cellatlas
Edit on GitHub
neuralib.atlas.cellatlas
Modules:
neuralib.atlas.cellatlas.core