Nucl.eye.D

Here you can find all datasets, scripts and trained models related to the Nucl.eye.D workflow presented in the publication - "Advanced image analysis methods for automated segmentation of subnuclear chromatin domains " !

The folder nucleyed.zip contains:  - trained models (>Output>models) 
                                                       - training data-set (>Input)
                                                       - all images (>Input)

The folder SupplementalMacros.zip contains all supplemental macro used for the analysis. 

The file : The_Nucl_Eye_D.ipynb can be directly used following the noted instructions :

- Download The_Nucl_Eye_D.ipynb 
- upload it to your Google Drive 
- Open it with Google Colaboratory (Or if not already installed : Open with -> More applications -> Google Colaboratory -> Install)

(We recommend using Chrome browser)

With the updated from 08.04.2024 the folder "H3K9me2 and H3K27me1 segmentation models.zip" was added - containing models for segmentation of H3K9me2 or H3K27me1 immunostained nuclei. Training sets are also contained. 

For question about the script contact : nucl.eye.d@gmail.com

Enjoy using Nucl.eye.D !