diff --git a/README.md b/README.md index 3f94fea4b8abdbba4c7a391ef4832824392df18c..cc06fb56f091b9f531159b15965d758836802e06 100644 --- a/README.md +++ b/README.md @@ -1,16 +1,10 @@ -# Code & Data Repository +# Code, Models & Data Repository ## *μPIX : Leveraging Generative AI for Enhanced, Personalized and Sustainable Microscopy* -### Gabriel Bon, Daniel Sapede, Cédric Matthews, and Fabrice Daian - ----- ----- - -| | Paper | -|--------------------------|--------------------------------------------------------------------------------------------------------------------------------| -| Preprint | [](https://doi.org/10.1101/2024.10.25.620201) | -| Paper | To be published | +Preprint BioRXiv [](https://doi.org/10.1101/2024.10.25.620201) +#### Gabriel Bon, Daniel Sapede, Cédric Matthews, and Fabrice Daian +##### <u>Dataset & pre-trained µPIX Models</u> | | Dataset | pre-trained µPIX Models | |--------------------------|--------------------------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------| | CSBDeep | [download](https://sync.lis-lab.fr/index.php/s/sy3SrGgqNafbP5X/download) | [download](https://sync.lis-lab.fr/index.php/s/9SxkR2QH3Z79Bbc/download) | @@ -18,11 +12,17 @@ | 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 | | -|--------------------------|--------------------------------------------------------------------------------------------------------------------------------| -| Inference on Metrology dataset using pre-trained µPIX model | [](https://colab.research.google.com/drive/1EbV04iv141q7ebVUOErJupYboaCV40OD?usp=drive_link) | +##### <u>Demo Notebooks</u> + +* Use a pre-trained µPIX model to denoise images (metrology dataset) [](https://colab.research.google.com/drive/1EbV04iv141q7ebVUOErJupYboaCV40OD?usp=drive_link) +* Train a µPIX model from scratch (metrology dataset) -| | Code & System Requirements | + +## Install required µPIX Environment and Sources ([Tutorial VIDEO](https://sync.lis-lab.fr/index.php/s/GeNyYdLHMCRTfS9)) +<details> + <summary>Click to expand</summary> + +| Requirements | | |--------------------------|--------------------------------------------------------------------------------------------------------------------------------| | Python | 3.11 | | Tensorflow | 2.14 | @@ -30,10 +30,6 @@ | OS | Linux | ----- ----- - -## Install required µPIX Environment and Sources ([Tutorial VIDEO](https://sync.lis-lab.fr/index.php/s/GeNyYdLHMCRTfS9)) @@ -61,7 +57,7 @@ and then proceed to the installation of required Python packages: ```bash pip install -r mupix/requirements.txt ``` - +</details> @@ -69,6 +65,9 @@ pip install -r mupix/requirements.txt ## Use Case n°1 - Use a pre-trained µPIX model to denoise an image dataset ([Tutorial VIDEO](https://sync.lis-lab.fr/index.php/s/ftw9fdGacJyyfBq)) +<details> + <summary>Click to expand</summary> + µPIX comes with 3 ptre-trained models along with their respective datasets: | | Dataset | pre-trained µPIX Models | @@ -174,9 +173,14 @@ python mupixinfer.py --experiment_path "./experiments/metrology_experiment/" Once finished, the denoised images are stored inside ```./experiments/metrology_experiment/predictions/``` directory. +</details> + ## Use case n°2 - Train a µPIX model from scratch using a custom dataset +<details> + <summary>Click to expand</summary> + Move to the `mupix` directory: ```bash cd mupix @@ -348,8 +352,6 @@ If the training stops because it reached the maximum number of epochs defined in python mupixtraining.py --experiment_path "./experiments/metrology_experiment" --retrain ``` - - ### 2.4 - Inference on the test dataset The `mupixinfer.py` script allows you to use a pre-trained µPIX model to denoise a dataset located in the `test` directory inside the experiment path. @@ -374,7 +376,7 @@ Saved prediction: ./experiments/metrology_experiment/predictions/X_StageData0001 All predictions saved successfully! Data predicted at ./experiments/metrology_experiment/predictions ! ``` - +</details>