diff --git a/.gitignore b/.gitignore index a2e6f722e354615840b9960caed2f992e3bc013f..b0acea42c3ab6e116934e69b296e8554e8fde2f7 100755 --- a/.gitignore +++ b/.gitignore @@ -114,4 +114,7 @@ venv.bak/ Part1Unet/models Part1Unet/logs Part1Unet/unet_model.png +Part1Unet/unet_full.ipynb Part2Cellpose/models +Part2Cellpose/train_cellpose_full.ipynb +Part2Cellpose/use_cellpose_full.ipynb \ No newline at end of file diff --git a/Part1Unet/README.md b/Part1Unet/README.md index 2f98731cf283cf4bfc3baaf6fd7b8acac4505192..ad306dd142887e969d3d25abd79995f9f6c285b8 100644 --- a/Part1Unet/README.md +++ b/Part1Unet/README.md @@ -1,17 +1,12 @@ -# Unet +# U-Net -Install unet env in conda +To run the notebook: ``` setconda -conda env create -f unet_env.yml -``` - -Launch the jupyter notebook - -``` -setconda -conda activate qlife25-unet +conda activate /users/bioensei/mphan/.conda/envs/qlife25-unet setenv LD_LIBRARY_PATH "${CONDA_PREFIX}/lib:${LD_LIBRARY_PATH}" jupyter notebook ``` + + diff --git a/Part2Cellpose/README.md b/Part2Cellpose/README.md index 5a33a7a2d1f75d87d812f1944af0b339ffd3e41a..7628f66268260b9eddc68b386f79740affd8b479 100644 --- a/Part2Cellpose/README.md +++ b/Part2Cellpose/README.md @@ -1,21 +1,9 @@ # Cellpose -Run the following commands to install cellpose env in conda +To run the notebook: ``` setconda -conda create -n qlife25-cellpose python=3.10 -y -conda activate qlife-cellpose -conda install pytorch==1.12.0 cudatoolkit=11.3 -c pytorch -pip uninstall torch -pip install 'cellpose[gui]' -pip install notebook==6.1.5 scikit-image matplotlib -``` - -Launch the jupyter notebook - -``` -setconda -conda activate qlife25-cellpose +conda activate /users/bioensei/mphan/.conda/envs/qlife25-cellpose jupyter notebook ``` \ No newline at end of file diff --git a/README.md b/README.md index c699df83d0f219bfcccd6218f63c3f32392dff64..488446b47e91667c77ee781a4b0801d2f94e8222 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,10 @@ -# 2025_qlife_psl_dl_course +# PSL Qlife Quantitative Biology Spring School 2025 -Materials for the course cellular segmentation with deep learning. \ No newline at end of file +Materials for the course *cellular segmentation with deep learning*. + +The course is organized in two parts: + +- Part 1: Semantic segmentation with U-Net. +- Part 2: Instance segmentation with Cellpose. + +Please download and unzip this repo to your local. \ No newline at end of file