From ca6465296a5e3f336b8563704aec28fffc32a6be Mon Sep 17 00:00:00 2001
From: laynholt <ne.free532@gmail.com>
Date: Fri, 9 May 2025 21:38:47 +0000
Subject: [PATCH] added references

---
 README.md              | 23 ++++++++++++++++++++++-
 core/segmentator.py    |  9 +++++++++
 core/utils/measures.py |  5 ++---
 3 files changed, 33 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index b2e5c1c..9e391b0 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,7 @@
 # Cell Segmentator
 
+---
+
 ## Overview
 
 This repository provides two main scripts to configure and run a cell segmentation workflow:
@@ -7,6 +9,8 @@ This repository provides two main scripts to configure and run a cell segmentati
 * **generate\_config.py**: Interactive script to create JSON configuration files for training or prediction.
 * **main.py**: Entry point to train, test, or predict using the generated configuration.
 
+---
+
 ## Installation
 
 0. **Install uv**:
@@ -40,6 +44,8 @@ Follow the official guide at [https://docs.astral.sh/uv/](https://docs.astral.sh
    uv sync
    ```
 
+---
+
 ## Dataset Structure
 
 Your data directory must follow this hierarchy:
@@ -75,6 +81,8 @@ In this case, set the `masks_subdir` field in your dataset configuration to the
 
 **Mask format**: Instance masks should be provided for multi-label segmentation with channel-last ordering, i.e., each mask array must have shape `(H, W, C)`.
 
+---
+
 ## generate\_config.py
 
 This script guides you through creating a JSON configuration for either training or prediction.
@@ -101,6 +109,8 @@ Generated config includes sections:
 * `wandb_config`: Weights & Biases integration settings
 * *(If training)* `criterion`, `optimizer`, `scheduler`
 
+---
+
 ## main.py
 
 Entrypoint to run training, testing, or prediction using a config file.
@@ -125,6 +135,8 @@ python main.py [-c CONFIG] [-m {train,test,predict}] [--no-save-masks] [--only-m
 5. **Run** training or inference (`.run()`).
 6. **Save** model checkpoint and upload to W\&B if in training mode.
 
+---
+
 ## Configurable Parameters
 
 A brief overview of the key parameters you can adjust in your JSON config:
@@ -155,6 +167,8 @@ A brief overview of the key parameters you can adjust in your JSON config:
 
 > **Batch size note:** Validation, testing, and prediction runs always use a batch size of `1`, regardless of the `batch_size` setting in the training configuration.
 
+---
+
 ## Examples
 
 ### Generate a training config
@@ -177,4 +191,11 @@ python main.py -c config/templates/train/YourConfig.json -m train
 python main.py -c config/templates/predict/YourConfig.json -m predict
 ```
 
----
\ No newline at end of file
+---
+
+## Acknowledgments
+
+This project was developed building upon the following open-source repositories:
+
+* [Cellpose](https://github.com/MouseLand/cellpose) by the MouseLand Lab.
+* [MEDIAR](https://github.com/Lee-Gihun/MEDIAR) by Lee Gihun.
diff --git a/core/segmentator.py b/core/segmentator.py
index 52e3575..a93f20b 100644
--- a/core/segmentator.py
+++ b/core/segmentator.py
@@ -1,3 +1,12 @@
+"""
+This code is adapted from the following codes:
+[1] https://github.com/MouseLand/cellpose/blob/main/cellpose/utils.py
+[2] https://github.com/MouseLand/cellpose/blob/main/cellpose/dynamics.py
+[3] https://github.com/MouseLand/cellpose/blob/main/cellpose/metrics.py
+[4] https://github.com/Lee-Gihun/MEDIAR/tree/main/core
+[5] https://github.com/Lee-Gihun/MEDIAR/tree/main/core/MEDIAR
+"""
+
 import random
 import numpy as np
 from numba import njit, prange
diff --git a/core/utils/measures.py b/core/utils/measures.py
index ffe1fba..c628a0c 100644
--- a/core/utils/measures.py
+++ b/core/utils/measures.py
@@ -1,7 +1,6 @@
 """
-Adapted from:
-[1] https://github.com/JunMa11/NeurIPS-CellSeg/blob/main/baseline/compute_metric.py
-[2] https://github.com/stardist/stardist/blob/master/stardist/matching.py
+This code is adapted from the following codes:
+[1] https://github.com/Lee-Gihun/MEDIAR/blob/main/train_tools/measures.py
 """
 
 import numpy as np