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
  • Parser
  • Edit on GitHub

Parser

Parsers for various neuroscience data formats and analysis tool outputs.

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
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© Copyright 2024, Yu-Ting Wei. Last updated on 2026-05-27.

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