Nikos Tsiknakis's repositories
multiresolution-clam
This is the repo for our EMBC-2023 paper, "Multiresolution Self-Supervised Feature Integration via Attention Multiple Instance Learning for Histopathology Analysis"
alvis-intro
Introduction slides for Alvis
Atten_Deep_MIL
Attention-based Deep MIL implementation and application
AttentionDeepMIL
Implementation of Attention-based Deep Multiple Instance Learning in PyTorch
pytorch_models
A collection of pytorch models and utility methods that I use for any deep-learning project.
tsik.me
My personal website powered by Jekyll and al-folio.
CLAM
Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering
DeepLearningExamples
Deep Learning Examples
DeepPATH
Classification of Lung cancer slide images using deep-learning
evaluateCutpoints
evaluateCutpoints is a R package for multiple cutpoints determination in biomedical research.
hass-config
✨ A different take on designing a Lovelace UI (Dashboard)
he_preprocessing
A collection of preprocessing tools for H&E slide analysis, developed and used for my PhD project.
histocartography
Histocartography is a framework bringing together AI and Digital Pathology
machine-learning-articles
🧠💬 Articles I wrote about machine learning, archived from MachineCurve.com.
Machine-Learning-Collection
A resource for learning about ML, DL, PyTorch and TensorFlow. Feedback always appreciated :)
multiresolution_histopathology
Code for paper: "Unveiling the Power of Model-Agnostic Multiscale Analysis for Enhancing Artificial Intelligence Models in Breast Cancer Histopathology Images"
NeighborhoodCoordination
Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front"
pathology-snippets
Pieces of code likely to be useful as part of larger projects
pathology-streaming-pipeline
Use streaming to train whole-slides images with single image-level labels, by reducing GPU memory requirements with 99%.
pathology-whole-slide-data
A package for working with whole-slide data including a fast batch iterator that can be used to train deep learning models.
ProLesA-Net
The current repository serves as the placeholder for the ProLesA-Net model
PytorchDigitalPathology
An implementation of Unet for pytorch designed for digital pathology segmentation
QuPath-IntelliJ-Template
This is a template project for QuPath development on IntelliJ
spams-python
A rehost of the python version of SPArse Modeling Software (SPAMS)
stainlib
Python 3 library for the augmentation & normalization of H&E images
XAI
Papers and code of Explainable AI esp. w.r.t. Image classificiation