OrgLine, the first multitask analysis pipeline for organoids, which leverages a pretrained detector and a vision foundational model to facilitate large-scale automated cultivation and analysis of organoids. OrgLine achieves precise localization, counting, classification, and segmentation of organoids, providing a foundational and efficient analytical support system.
-
Environment Setup Configuration
Automatic environment setup, please be patient.
conda create -n orgline python=3.10 conda activate orgline conda install git git clone https://github.com/ucas-dx/OrgLine.git cd OrgLine python install_env.py conda install conda-forge::vs2015_runtime
-
Quick usage
cd models & python simple_inference.py
-
Jupyter
You can run the contents of the SimpleOperation.ipynb file, and all processes will be automated.
from models.simple_inference import OrgAnalysis image_folder = 'images' org_analysis = OrgAnalysis(image_folder) org_analysis.analyze(show_seg=True,show_bboxes=False)