# Copick-Torch Augmentation Examples

This document shows examples of various augmentations applied to the dataset used in the `spliced_mixup_example.py` example.

For each class, we show the original volume and various augmentations applied to it.
The visualizations show both central slices (top row) and sum projections (bottom row) in XY, XZ, and YZ planes.

## Class: virus-like-capsid

### Original

![virus-like-capsid - Original](./virus-like-capsid_original.png)

### Brightness (+0.5)

![virus-like-capsid - Brightness (+0.5)](./virus-like-capsid_brightness_+0.5.png)

### Brightness (-0.5)

![virus-like-capsid - Brightness (-0.5)](./virus-like-capsid_brightness_-0.5.png)

### Gaussian Blur (σ=1.0)

![virus-like-capsid - Gaussian Blur (σ=1.0)](./virus-like-capsid_gaussian_blur_σ1.0.png)

### Intensity Scaling (1.5x)

![virus-like-capsid - Intensity Scaling (1.5x)](./virus-like-capsid_intensity_scaling_1.5x.png)

### Intensity Scaling (0.5x)

![virus-like-capsid - Intensity Scaling (0.5x)](./virus-like-capsid_intensity_scaling_0.5x.png)

### Flip (Z axis)

![virus-like-capsid - Flip (Z axis)](./virus-like-capsid_flip_z_axis.png)

### Rotation (90°, XY plane)

![virus-like-capsid - Rotation (90°, XY plane)](./virus-like-capsid_rotation_90_xy_plane.png)

### Fourier Augmentation

![virus-like-capsid - Fourier Augmentation](./virus-like-capsid_fourier_augmentation.png)

## Class: background

### Original

![background - Original](./background_original.png)

### Brightness (+0.5)

![background - Brightness (+0.5)](./background_brightness_+0.5.png)

### Brightness (-0.5)

![background - Brightness (-0.5)](./background_brightness_-0.5.png)

### Gaussian Blur (σ=1.0)

![background - Gaussian Blur (σ=1.0)](./background_gaussian_blur_σ1.0.png)

### Intensity Scaling (1.5x)

![background - Intensity Scaling (1.5x)](./background_intensity_scaling_1.5x.png)

### Intensity Scaling (0.5x)

![background - Intensity Scaling (0.5x)](./background_intensity_scaling_0.5x.png)

### Flip (Z axis)

![background - Flip (Z axis)](./background_flip_z_axis.png)

### Rotation (90°, XY plane)

![background - Rotation (90°, XY plane)](./background_rotation_90_xy_plane.png)

### Fourier Augmentation

![background - Fourier Augmentation](./background_fourier_augmentation.png)

## Class: thyroglobulin

### Original

![thyroglobulin - Original](./thyroglobulin_original.png)

### Brightness (+0.5)

![thyroglobulin - Brightness (+0.5)](./thyroglobulin_brightness_+0.5.png)

### Brightness (-0.5)

![thyroglobulin - Brightness (-0.5)](./thyroglobulin_brightness_-0.5.png)

### Gaussian Blur (σ=1.0)

![thyroglobulin - Gaussian Blur (σ=1.0)](./thyroglobulin_gaussian_blur_σ1.0.png)

### Intensity Scaling (1.5x)

![thyroglobulin - Intensity Scaling (1.5x)](./thyroglobulin_intensity_scaling_1.5x.png)

### Intensity Scaling (0.5x)

![thyroglobulin - Intensity Scaling (0.5x)](./thyroglobulin_intensity_scaling_0.5x.png)

### Flip (Z axis)

![thyroglobulin - Flip (Z axis)](./thyroglobulin_flip_z_axis.png)

### Rotation (90°, XY plane)

![thyroglobulin - Rotation (90°, XY plane)](./thyroglobulin_rotation_90_xy_plane.png)

### Fourier Augmentation

![thyroglobulin - Fourier Augmentation](./thyroglobulin_fourier_augmentation.png)

## Class: beta-amylase

### Original

![beta-amylase - Original](./beta-amylase_original.png)

### Brightness (+0.5)

![beta-amylase - Brightness (+0.5)](./beta-amylase_brightness_+0.5.png)

### Brightness (-0.5)

![beta-amylase - Brightness (-0.5)](./beta-amylase_brightness_-0.5.png)

### Gaussian Blur (σ=1.0)

![beta-amylase - Gaussian Blur (σ=1.0)](./beta-amylase_gaussian_blur_σ1.0.png)

### Intensity Scaling (1.5x)

![beta-amylase - Intensity Scaling (1.5x)](./beta-amylase_intensity_scaling_1.5x.png)

### Intensity Scaling (0.5x)

![beta-amylase - Intensity Scaling (0.5x)](./beta-amylase_intensity_scaling_0.5x.png)

### Flip (Z axis)

![beta-amylase - Flip (Z axis)](./beta-amylase_flip_z_axis.png)

### Rotation (90°, XY plane)

![beta-amylase - Rotation (90°, XY plane)](./beta-amylase_rotation_90_xy_plane.png)

### Fourier Augmentation

![beta-amylase - Fourier Augmentation](./beta-amylase_fourier_augmentation.png)

## Class: ferritin-complex

### Original

![ferritin-complex - Original](./ferritin-complex_original.png)

### Brightness (+0.5)

![ferritin-complex - Brightness (+0.5)](./ferritin-complex_brightness_+0.5.png)

### Brightness (-0.5)

![ferritin-complex - Brightness (-0.5)](./ferritin-complex_brightness_-0.5.png)

### Gaussian Blur (σ=1.0)

![ferritin-complex - Gaussian Blur (σ=1.0)](./ferritin-complex_gaussian_blur_σ1.0.png)

### Intensity Scaling (1.5x)

![ferritin-complex - Intensity Scaling (1.5x)](./ferritin-complex_intensity_scaling_1.5x.png)

### Intensity Scaling (0.5x)

![ferritin-complex - Intensity Scaling (0.5x)](./ferritin-complex_intensity_scaling_0.5x.png)

### Flip (Z axis)

![ferritin-complex - Flip (Z axis)](./ferritin-complex_flip_z_axis.png)

### Rotation (90°, XY plane)

![ferritin-complex - Rotation (90°, XY plane)](./ferritin-complex_rotation_90_xy_plane.png)

### Fourier Augmentation

![ferritin-complex - Fourier Augmentation](./ferritin-complex_fourier_augmentation.png)

## Class: beta-galactosidase

### Original

![beta-galactosidase - Original](./beta-galactosidase_original.png)

### Brightness (+0.5)

![beta-galactosidase - Brightness (+0.5)](./beta-galactosidase_brightness_+0.5.png)

### Brightness (-0.5)

![beta-galactosidase - Brightness (-0.5)](./beta-galactosidase_brightness_-0.5.png)

### Gaussian Blur (σ=1.0)

![beta-galactosidase - Gaussian Blur (σ=1.0)](./beta-galactosidase_gaussian_blur_σ1.0.png)

### Intensity Scaling (1.5x)

![beta-galactosidase - Intensity Scaling (1.5x)](./beta-galactosidase_intensity_scaling_1.5x.png)

### Intensity Scaling (0.5x)

![beta-galactosidase - Intensity Scaling (0.5x)](./beta-galactosidase_intensity_scaling_0.5x.png)

### Flip (Z axis)

![beta-galactosidase - Flip (Z axis)](./beta-galactosidase_flip_z_axis.png)

### Rotation (90°, XY plane)

![beta-galactosidase - Rotation (90°, XY plane)](./beta-galactosidase_rotation_90_xy_plane.png)

### Fourier Augmentation

![beta-galactosidase - Fourier Augmentation](./beta-galactosidase_fourier_augmentation.png)

## Class: cytosolic-ribosome

### Original

![cytosolic-ribosome - Original](./cytosolic-ribosome_original.png)

### Brightness (+0.5)

![cytosolic-ribosome - Brightness (+0.5)](./cytosolic-ribosome_brightness_+0.5.png)

### Brightness (-0.5)

![cytosolic-ribosome - Brightness (-0.5)](./cytosolic-ribosome_brightness_-0.5.png)

### Gaussian Blur (σ=1.0)

![cytosolic-ribosome - Gaussian Blur (σ=1.0)](./cytosolic-ribosome_gaussian_blur_σ1.0.png)

### Intensity Scaling (1.5x)

![cytosolic-ribosome - Intensity Scaling (1.5x)](./cytosolic-ribosome_intensity_scaling_1.5x.png)

### Intensity Scaling (0.5x)

![cytosolic-ribosome - Intensity Scaling (0.5x)](./cytosolic-ribosome_intensity_scaling_0.5x.png)

### Flip (Z axis)

![cytosolic-ribosome - Flip (Z axis)](./cytosolic-ribosome_flip_z_axis.png)

### Rotation (90°, XY plane)

![cytosolic-ribosome - Rotation (90°, XY plane)](./cytosolic-ribosome_rotation_90_xy_plane.png)

### Fourier Augmentation

![cytosolic-ribosome - Fourier Augmentation](./cytosolic-ribosome_fourier_augmentation.png)

## Dataset Information

The dataset used in this example is created using the `SplicedMixupDataset` class with the following parameters:

```python
dataset = SplicedMixupDataset(
    exp_dataset_id=10440,         # Experimental dataset ID
    synth_dataset_id=10441,       # Synthetic dataset ID
    synth_run_id="16487",         # Synthetic run ID
    overlay_root="/tmp/test/",    # Overlay root directory
    boxsize=(48, 48, 48),         # Size of the subvolumes
    augment=True,                 # Enable basic augmentations
    cache_dir='./cache',          # Cache directory
    cache_format='parquet',       # Cache format
    voxel_spacing=10.012,         # Voxel spacing
    include_background=True,      # Include background samples
    background_ratio=0.2,         # Background ratio
    min_background_distance=48,   # Minimum distance from particles for background
    blend_sigma=2.0,              # Controls Gaussian blending at boundaries
    mixup_alpha=0.2,              # Alpha parameter for mixup
    max_samples=100               # Maximum number of samples to generate
)
```

### Class Distribution

| Class | Count |
|-------|-------|
| background | 50 |
| cytosolic-ribosome | 11 |
| beta-galactosidase | 12 |
| beta-amylase | 6 |
| thyroglobulin | 5 |
| ferritin-complex | 8 |
| virus-like-capsid | 8 |
