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CAREamics

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CAREamics

GitHub

Home
Installation
Installation
Features
Guides
Guides
- CAREamist API
  CAREamist API
  - Configuration
    
    Configuration
    
    Convenience functions
    
    Save and load
    
    Custom types
    
    Configuration errors
    
    Build the configuration
    
    Algorithm requirements
  - Using CAREamics
    
    Using CAREamics
    
    CAREamist
    
    Training
    
    (Intermediate) Datasets
    
    Prediction
    
    Export to BMZ
  - FAQ
- Lightning API
  Lightning API
- napari plugin
  napari plugin
- Dev resources
  Dev resources
API Reference
API Reference
- Careamics
- Careamist
- Nm Training Placeholder
- Cli
  Cli
  - Conf
  - Main
  - Utils
- Config
  Config
  - Configuration
  - Configuration Factories
  - Algorithms
    
    Algorithms
    
    CARE Algorithm Config
    
    HDN Algorithm Config
    
    Microsplit Algorithm Config
    
    N2N Algorithm Config
    
    N2V Algorithm Config
    
    PN2V Algorithm Config
    
    UNet Algorithm Config
    
    VAE Algorithm Config
  - Architectures
    
    Architectures
    
    Architecture Config
    
    LVAE Config
    
    UNet Config
  - Augmentations
    
    Augmentations
    
    N2V Manipulate Config
    
    Normalize Config
    
    Transform Config
    
    Transform Unions
    
    XY Flip Config
    
    XY Random Rotate90 Config
  - Data
    
    Data
    
    Data Config
    
    Inference Config
    
    Normalization Config
    
    Tile Information
  - Lightning
    
    Lightning
    
    Optimizer Configs
    
    Training Config
    
    Callbacks
    
    Callbacks
    
    Callback Config
  - Losses
    
    Losses
    
    Loss Config
  - Noise Model
    
    Noise Model
    
    Likelihood Config
    
    Noise Model Config
  - Support
    
    Support
    
    Supported Activations
    
    Supported Algorithms
    
    Supported Architectures
    
    Supported Data
    
    Supported Filters
    
    Supported Loggers
    
    Supported Losses
    
    Supported Normalization
    
    Supported Optimizers
    
    Supported Patching Strategies
    
    Supported Pixel Manipulations
    
    Supported Struct Axis
    
    Supported Transforms
  - Utils
    
    Utils
    
    Configuration IO
    
    Random
  - Validators
    
    Validators
    
    Axes Validators
    
    Model Validators
    
    Patch Validators
- Dataset
  Dataset
  - In Memory Dataset
  - In Memory Pred Dataset
  - In Memory Tiled Pred Dataset
  - Iterable Dataset
  - Iterable Pred Dataset
  - Iterable Tiled Pred Dataset
  - Dataset Utils
    
    Dataset Utils
    
    File Utils
    
    Iterate Over Files
    
    Running Stats
  - Patching
    
    Patching
    
    Patching
    
    Random Patching
    
    Sequential Patching
    
    Validate Patch Dimension
  - Tiling
    
    Tiling
    
    Collate Tiles
    
    LVAE Tiled Patching
    
    Tiled Patching
- File IO
  File IO
  - Read
    
    Read
    
    Get Func
    
    Tiff
  - Write
    
    Write
    
    Get Func
    
    Tiff
- Lightning
  Lightning
  - Lightning Module
  - Microsplit Data Module
  - Predict Data Module
  - Train Data Module
  - Callbacks
    
    Callbacks
    
    Careamics Checkpoint Info Callback
    
    Data Stats Callback
    
    Hyperparameters Callback
    
    Progress Bar Callback
    
    Stop Prediction Callback
    
    Prediction Writer Callback
    
    Prediction Writer Callback
    
    File Path Utils
    
    Prediction Writer Callback
    
    Write Strategy
    
    Write Strategy Factory
- Losses
  Losses
  - Loss Factory
  - FCN
    
    FCN
    
    Losses
  - LVAE
    
    LVAE
    
    Loss Utils
    
    Losses
- LVAE Training
  LVAE Training
  - Calibration
  - Eval Utils
  - Get Config
  - Lightning Module
  - Metrics
  - Train LVAE
  - Train Utils
  - Dataset
    
    Dataset
    
    Config
    
    Lc Dataset
    
    Ms Dataset Ref
    
    Multich Dataset
    
    Multicrop Dset
    
    Multifile Dataset
    
    Types
    
    Utils
    
    Utils
    
    Data Utils
    
    Empty Patch Fetcher
    
    Index Manager
    
    Index Switcher
- Model IO
  Model IO
  - Bmz IO
  - Model IO Utils
  - Bioimage
    
    Bioimage
    
    Bioimage Utils
    
    Cover Factory
    
    Model Description
- Models
  Models
  - Activation
  - Layers
  - Model Factory
  - UNet
  - LVAE
    
    LVAE
    
    Layers
    
    Likelihoods
    
    LVAE
    
    Noise Models
    
    Stochastic
    
    Utils
- Prediction Utils
  Prediction Utils
- Transforms
  Transforms
- Utils
  Utils
  - Autocorrelation
  - Base Enum
  - Context
  - Deprecation
  - Lightning Utils
  - Logging
  - Metrics
  - Path Utils
  - Plotting
  - Ram
  - Receptive Field
  - Reshape Array
  - Serializers
  - Torch Utils
  - Version

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