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Commit 14d49cbf authored by Fabrice Daian's avatar Fabrice Daian
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...@@ -12,17 +12,22 @@ Preprint BioRXiv [![DOI:10.1101/2024.10.25.620201](images/badge_preprint_mupix.s ...@@ -12,17 +12,22 @@ Preprint BioRXiv [![DOI:10.1101/2024.10.25.620201](images/badge_preprint_mupix.s
| ```metrology``` | [download](https://sync.lis-lab.fr/index.php/s/mYDRTeAQxMxNPPJ/download) | [download](https://sync.lis-lab.fr/index.php/s/degZsCxN7ZXxeB6/download) | | ```metrology``` | [download](https://sync.lis-lab.fr/index.php/s/mYDRTeAQxMxNPPJ/download) | [download](https://sync.lis-lab.fr/index.php/s/degZsCxN7ZXxeB6/download) |
#### ```Demo Notebooks on Google Colab```
* **Use Case n°1:** Use a pre-trained µPIX model to denoise an image dataset (```metrology``` dataset) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1EbV04iv141q7ebVUOErJupYboaCV40OD?usp=drive_link) |```Demo Notebooks on Google Colab``` | | |
* **Use Case n°2:** Train a µPIX model from scratch using a custom dataset (```metrology``` dataset) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1GaD6rjWGJsBr2dFy-WPLC3YjCZO4LJGl?usp=drive_link) |---|---|---|
| **Use case #1** | Use a pre-trained µPIX model to denoise an image dataset (```metrology``` dataset) | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1EbV04iv141q7ebVUOErJupYboaCV40OD?usp=drive_link)
| **Use case #2** | Train a µPIX model from scratch using a custom dataset (```metrology``` dataset) | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1GaD6rjWGJsBr2dFy-WPLC3YjCZO4LJGl?usp=drive_link)
#### ```Reproductibility ```
* **Code supporting Tables and Figures:** [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1x1NtdC0b-vgsjWv0oUbeRzDLmDwv6NiV?usp=drive_link)
## Install µPIX Environment and Sources ([Tutorial VIDEO](https://sync.lis-lab.fr/index.php/s/GeNyYdLHMCRTfS9)) |```Reproductibility ``` | |
|---|---|
|**Ready-to-use Notebook supporting Tables and Figures presented in the paper** |[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1x1NtdC0b-vgsjWv0oUbeRzDLmDwv6NiV?usp=drive_link)|
## Install µPIX Environment and Sources ([Tutorial 🎬](https://sync.lis-lab.fr/index.php/s/GeNyYdLHMCRTfS9))
<details> <details>
<summary>Click to expand</summary> <summary>Click to expand</summary>
...@@ -35,8 +40,6 @@ Preprint BioRXiv [![DOI:10.1101/2024.10.25.620201](images/badge_preprint_mupix.s ...@@ -35,8 +40,6 @@ Preprint BioRXiv [![DOI:10.1101/2024.10.25.620201](images/badge_preprint_mupix.s
If you do not have already miniconda installed on your system, please refer to the [officical miniconda documentation](https://docs.anaconda.com/miniconda/install/). Then : If you do not have already miniconda installed on your system, please refer to the [officical miniconda documentation](https://docs.anaconda.com/miniconda/install/). Then :
1- Create a miniconda environment and source it: 1- Create a miniconda environment and source it:
...@@ -68,7 +71,7 @@ pip install -r mupix/requirements.txt ...@@ -68,7 +71,7 @@ pip install -r mupix/requirements.txt
## Use Case #1 - Use a pre-trained µPIX model to denoise an image dataset ([Tutorial VIDEO](https://sync.lis-lab.fr/index.php/s/ftw9fdGacJyyfBq)) ## Use Case #1 - Use a pre-trained µPIX model to denoise an image dataset ([Tutorial 🎬](https://sync.lis-lab.fr/index.php/s/ftw9fdGacJyyfBq))
<details> <details>
<summary>Click to expand</summary> <summary>Click to expand</summary>
...@@ -181,7 +184,8 @@ Once completed, the denoised images are stored in the ```./experiments/metrology ...@@ -181,7 +184,8 @@ Once completed, the denoised images are stored in the ```./experiments/metrology
</details> </details>
## Use Case #2 - Train a µPIX model from scratch using a custom dataset ## Use Case #2 - Train a µPIX model from scratch using a custom dataset ([Tutorial 🎬](https://sync.lis-lab.fr/index.php/s/pb5jPqNtTgwFSjB))
<details> <details>
<summary>Click to expand</summary> <summary>Click to expand</summary>
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