From cbcbe2b2c9a8d98faf013c22e533b8e17137cf3f Mon Sep 17 00:00:00 2001
From: Son Phan <msphan@outlook.com>
Date: Thu, 27 Mar 2025 14:03:56 +0100
Subject: [PATCH] update READMEs

---
 .gitignore              |  3 +++
 Part1Unet/README.md     | 15 +++++----------
 Part2Cellpose/README.md | 16 ++--------------
 README.md               | 11 +++++++++--
 4 files changed, 19 insertions(+), 26 deletions(-)

diff --git a/.gitignore b/.gitignore
index a2e6f72..b0acea4 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 2f98731..ad306dd 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 5a33a7a..7628f66 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 c699df8..488446b 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
-- 
GitLab