diff --git a/tutorials/4-developers/DTDV401_overview.ipynb b/tutorials/4-developers/DTDV401_overview.ipynb index 9bb7dd1e3..61ab9d2d4 100644 --- a/tutorials/4-developers/DTDV401_overview.ipynb +++ b/tutorials/4-developers/DTDV401_overview.ipynb @@ -303,19 +303,19 @@ "source": [ "All the classes in the following modules extend `Feature` and represent transformations in some way:\n", "\n", - "- [scatterers.py](https://github.com/DeepTrackAI/DeepTrack2/blob/develop/deeptrack/scatterers.py) provides a framework for implementing light-scattering objects.\n", + "- [scatterers.py](https://github.com/DeepTrackAI/DeepTrack2/blob/develop/deeptrack/optical/scatterers.py) provides a framework for implementing light-scattering objects.\n", "\n", - "- [optics.py](https://github.com/DeepTrackAI/DeepTrack2/blob/develop/deeptrack/optics.py) provides a framework for simulating the optics of a variety of microscopy setups such as darkfield, fluorescence, or brightfield, as well as for incorporating the interaction between a sample (often a scatterer object) and a microscopy setup.\n", + "- [optics.py](https://github.com/DeepTrackAI/DeepTrack2/blob/develop/deeptrack/optical/optics.py) provides a framework for simulating the optics of a variety of microscopy setups such as darkfield, fluorescence, or brightfield, as well as for incorporating the interaction between a sample (often a scatterer object) and a microscopy setup.\n", "\n", - "- [holography.py](https://github.com/DeepTrackAI/DeepTrack2/blob/develop/deeptrack/holography.py) provides features for managing optical fields with Fourier transforms and propagation matrices for usage in simulation pipelines and holographic reconstructions.\n", + "- [holography.py](https://github.com/DeepTrackAI/DeepTrack2/blob/develop/deeptrack/optical/holography.py) provides features for managing optical fields with Fourier transforms and propagation matrices for usage in simulation pipelines and holographic reconstructions.\n", "\n", - "- [aberrations.py](https://github.com/DeepTrackAI/DeepTrack2/blob/develop/deeptrack/aberrations.py) provides a framework to simulate optical aberrations in microscopy setups by implementing Zernike polynomials and Gaussian pupil apodization.\n", + "- [aberrations.py](https://github.com/DeepTrackAI/DeepTrack2/blob/develop/deeptrack/optical/aberrations.py) provides a framework to simulate optical aberrations in microscopy setups by implementing Zernike polynomials and Gaussian pupil apodization.\n", "\n", - "- [augmentations.py](https://github.com/DeepTrackAI/DeepTrack2/blob/develop/deeptrack/augmentations.py) provides a framework to augment data with various transformations and image manipulation techniques such as rotations, deformations, cropping, padding.\n", + "- [augmentations.py](https://github.com/DeepTrackAI/DeepTrack2/blob/develop/deeptrack/optical/augmentations.py) provides a framework to augment data with various transformations and image manipulation techniques such as rotations, deformations, cropping, padding.\n", "\n", - "- [noises.py](https://github.com/DeepTrackAI/DeepTrack2/blob/develop/deeptrack/noises.py) provides a framework to add various types of additive noise to images as well as Poisson noise based on signal-to-noise ratio.\n", + "- [noises.py](https://github.com/DeepTrackAI/DeepTrack2/blob/develop/deeptrack/optical/noises.py) provides a framework to add various types of additive noise to images as well as Poisson noise based on signal-to-noise ratio.\n", "\n", - "- [math.py](https://github.com/DeepTrackAI/DeepTrack2/blob/develop/deeptrack/math.py) provides utilities for various types of normalization, blurring, pooling, and resizing of images." + "- [math.py](https://github.com/DeepTrackAI/DeepTrack2/blob/develop/deeptrack/optical/math.py) provides utilities for various types of normalization, blurring, pooling, and resizing of images." ] }, {