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giovannivolpe merged 2 commits into from
Jul 14, 2026
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tutorials/4-developers fix optical directory links #505

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71724ec
fix: developer overview optical directory links
foca13 Jul 14, 2026
5db0949
Merge branch 'develop' into fix-developers-overview-links
foca13 Jul 14, 2026
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14 changes: 7 additions & 7 deletions tutorials/4-developers/DTDV401_overview.ipynb
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Expand Up @@ -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."
]
},
{
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