Name: Alberto Diez, PhD
Type: User
Company: NTNU, Centre for Molecular Inflammation Research (CEMIR)
Bio: Passionate about peering into the microscopic world š¬
š»š Python coder by day, data enthusiast by night š
āļøW40K nerd
Location: Trondheim, Norway
Alberto Diez, PhD's Projects
This is just a practice repository to keep track of most of the projects I built during the 100 Days of Code course.
Config files for my GitHub profile.
Simple scripts to check xy alignment and dual cam colocalization in the Nikon Crestoptics V3 system at CMIC@NTNU
Lecture materials "Bio-image analysis, biostatistics, programming and machine learning for computational biology" at the Center of Molecular and Cellular Bioengineering (CMCB) / University of Technology, TU Dresden
Analysis of brighfield images of colonoids growing in Matrigel droplets to extract morphological features and object counts.
Examples and tutorials on using SOTA computer vision models and techniques. Learn everything from old-school ResNet, through YOLO and object-detection transformers like DETR, to the latest models like Grounding DINO and SAM.
Solutions to the webinar part of the 2023 EMBL Deep Learning for image analysis course.
Advanced methods in bioimage analysis bash OME
A series of Jupyter notebooks that walk you through the fundamentals of Machine Learning and Deep Learning in Python using Scikit-Learn, Keras and TensorFlow 2.
Tools to analyze intestinal organoid imaging at the Martin-Alonso/Oudhoff lab
Tools to analyze intestinal organoid imaging at the Martin-Alonso/Oudhoff lab using AI
Quick Jupyter notebook to go through folders containing .lsm files and performing a maximum intensity projection of the third fluorescent channel.
Python script to analyze DNA damage in microglial cells
Lectures for a napari training course
NEUBIAS Academy @Home: Interactive Bioimage Analysis with Python and Jupyter
Measuring intensity of two marker proteins inside the nucleus
Checking nuclear translocation of proteins using Voronoi-Otsu labeling and label erosion from pyclesperanto
This is the repository for a Python bioimage analysis course which establishes the fundamentals of image analysis in the context of biological imaging.
Collection of scripts to plot TPMs (Transcripts per Million) gene expression data from .csv RNASeq-derived files. Optimized for Google Collab.
Tutorial for SciPy 2021 Bioimage Analysis Fundamentals in Python
Semantic segmentation of healthy vs tumor tissue in mouse intestinal swiss rolls
Checking nuclear translocation of proteins using Voronoi-Otsu labeling and label erosion from pyclesperanto. Maybe Cellpose cyto (WIP)