To open hyperparameters settings, click Edit underneath the Hyperparameters dropdown menu to open a dialog where you can set custom hyperparameters.
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1. Network Type
This tab defines the deep learning network we would like to use.
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Options | Description |
|---|---|
RCAN | For denoising and super-resolution. This is also the model used by our Nature Methods papaerpaper. https://www.nature.com/articles/s41592-021-01155-x |
UNet | For virtual staining and segmentation. [1505.04597] U-Net: Convolutional Networks for Biomedical Image Segmentation (arxiv.org) |
Network Shape
Options: 2D or 3D
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How to use it: Increase it for model complexity, reduce it for a smaller model..
Number of Residual Groups
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How to use it: Increase it for model complexity, reduce it for a smaller model..
Channel Reduction Factor
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Description: Channel reduction factor for the squeeze-and-excitation module. See
How to use it: Increase channel reduction factor for better performance.
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How to use it: Increase it to build a more complex model, reduce it for reduce it for a smaller model.
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Options | Description | When to use |
|---|---|---|
None | Use the raw input to train deep learning models | Choose this option if you want to use the original data to train or your input images have been normalized (Note: If the image is 8-bit or 16-bit, the scripts will error out and ask users to choose one of the normalization methods.) |
Percentile | Normalize input images using percentile method. Normalizes the image intensity so that the 2nd and 99th percentiles are converted to 0 and 1 respectively. | Generally good for fluorescence images |
Divide by Max | Using the max intensity value to normalize images. | Useful for normalizing segmentation mask |
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Data Augmentation
Options | Description | When to use |
|---|---|---|
None | No augmentation | If you believe you have enough image pair samples |
Rotate_and_flip | Randomly rotate and flip data to increasing increase input data variety. Note that when this option is selected, you need to make sure the Block Size width and height is are the same. | If you have little a limited amount of data, allow allowing data augmentation generally gives you a better results and prevent prevents overfitting. |
Block Size
Default: 256, 256, 16 (width, height, depth)
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Options | Description | When to use |
|---|---|---|
Intensity threshold | If | Set the threshold when your images has have fewer foregroundforegrounds. Try to start with a small number such as 0.25. |
Area ratio threshold | If | Set the threshold when your images has have fewer foreground signals. Try to start with 0.05. |
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Options | Description | When to use |
|---|---|---|
Staircase exponential decay | drop the learning rate by half every | Default |
Exponential Decay | Exponentially reduce the learning rate on every epoch using the function: learning_rate = learning_rate*0.5^(epoch/100) | If staircase exponential decay does not works work for your model |
Reduce on Plateau | Reduce learning rate to 0.1*learning_rate when validation loss has stopped improving for more than 10 epochs. | For models that are harder to train. |
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Options | Description | When to use |
|---|---|---|
Mean absolute error | Measures the mean absolute error (MAE) between each element in the input x and target y.Default Prediction(Pred) and Ground Truth(GT). | The default for Denoising, Super-Resolution, and Virtual Staining |
balanced binary crossentropycross-entropy | Weighted verision version binary crossentropy cross-entropy loss for imbalanced data. | Default for Segmentation |
Mean squared error | Measures the mean squared error (MAE) between each element in the input x and target yPrediction(Pred) and Ground Truth(GT). | More sensitive to outlier comparing compared to mean absolute error. |
binary cross-entropy | BCE compares each of the predicted probabilities to binary Ground Truth | Good for segmentation, only when the data is balanced |
dice loss | 2*(Pred ∩ GT) / (Pred + GT) | Also good for imbalanced data |
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Options | Description | When to use |
|---|---|---|
PSNR | Computes the peak signal-to-noise ratio between two images. Note that the maximum signal value is assumed to be 1. | Denoising, Super-Resolution, and Virtual Staining |
SSIM | Computes the structural similarity index between two images. Note that the maximum signal value is assumed to be 1. | Denoising, Super-Resolution, and Virtual Staining |
Accuracy | Correct outputs/Total outputs | Segmentation |
3. Apply Parameters
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Intensity Normalization Method
Should It should be the same as the intensity normalization method in Training parameters.
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