Repositories list

• chromatin_ndd

  Public
  Code for bachelorsthesis of Dario "Evaluating the Potential of AI-Based Chromatin Imaging Analysis to detect Signals of Neurodegenerative Diseases"

  Jupyter Notebook

  •0•0•0•0•Updated Jul 15, 2024Jul 15, 2024

• germinal_center

  Public
  Python code for the chromatin state analyses of the paper

  Jupyter Notebook

  •1•1•0•0•Updated Feb 23, 2024Feb 23, 2024

• chrometrics

  Public
  Nuclear Morphology and Chromatin Organization Features

  computer-visiontexturefeature-extraction+ 4nucleusmorphological-analysismicroscopy-dataimage-features

  Jupyter Notebook

  •

  MIT License

  •5•4•0•0•Updated Feb 15, 2024Feb 15, 2024

• immune_cell_project

  Public
  Code for the manuscript: "Single-cell imaging-AI based chromatin biomarkers for proton therapy efficacy in tumor patients using liquid biopsies". Code was developed by Daniel Paysan

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Nov 13, 2023Nov 13, 2023

• genomic-scoring-breast-cancer-progression

  Public
  Project in which we use image based chromatin(NMCO) features to identify abnormal cells in TMA

  Jupyter Notebook

  •

  MIT License

  •1•1•0•0•Updated Nov 18, 2021Nov 18, 2021

• segmentation_evaluation

  Public
  Training and testing the nuclear segmentation.

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Sep 10, 2021Sep 10, 2021

• MobilePhone_Microscopy

  Public
  MATLAB

  •1•0•0•0•Updated Aug 30, 2021Aug 30, 2021

• annotate_images

  Public
  Interactively generate/edit segmentation labels using napari

  Python

  •

  MIT License

  •1•0•0•0•Updated Aug 26, 2021Aug 26, 2021

• nuclear_segmentation

  Public
  Nuclear segmentation of microscopy images

  Jupyter Notebook

  •1•0•0•0•Updated Sep 28, 2020Sep 28, 2020

• domain_translation

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Sep 22, 2020Sep 22, 2020

• Multivariate_analysis_cancer-activation-primed-geometries

  Public
  Multivariate analysis reveals activation-primed fibroblast geometric states in engineered 3D tumor microenvironments (Paper)

  MATLAB

  •1•0•0•0•Updated Sep 8, 2020Sep 8, 2020

• Cell_Shape_Compressive_Force_MBoC_2018

  Public
  Analysis used in Damodaran et.al, Molecular Biology of the Cell , 2018

  R

  •2•0•0•0•Updated Jul 19, 2020Jul 19, 2020

• Cell_Shape_TNF_alpha_PNAS_2017

  Public
  Analysis in the paper Mitra et.al. PNAS 2017.

  1•0•0•0•Updated Jul 19, 2020Jul 19, 2020

• Latterally_confined_growth_stem_cell_engineering_PNAS_2018

  Public
  Transcriptome Analysis performed for the Roy et.al PNAS 2018 Paper

  R

  •1•0•0•0•Updated Jul 18, 2020Jul 18, 2020

• Chromsome-intermingling-region-indentifcation-and-characterisation-of-protein-levels

  Public
  Analysis performed for the Belyaeva et.al PNAS 2017 Paper

  R

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Jul 18, 2020Jul 18, 2020