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100-days-of-code-python

This is just a practice repository to keep track of most of the projects I built during the 100 Days of Code course.

adiezsanchez

Config files for my GitHub profile.

bf_intorg_yolov8_dev

bio-image_analysis_with_python_2023

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

biofilm_meas

colon_organoid_bf

Analysis of brighfield images of colonoids growing in Matrigel droplets to extract morphological features and object counts.

cv-models-roboflow-2023

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.

embl-deep-learning-2023

Solutions to the webinar part of the 2023 EMBL Deep Learning for image analysis course.

embo-2023-bash-ome

Advanced methods in bioimage analysis bash OME

handson-ml3

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.

intestinal_organoid_brightfield_analysis

Tools to analyze intestinal organoid imaging at the Martin-Alonso/Oudhoff lab

intestinal_organoid_yolov8

Tools to analyze intestinal organoid imaging at the Martin-Alonso/Oudhoff lab using AI

lsm_zeiss_mip

Quick Jupyter notebook to go through folders containing .lsm files and performing a maximum intensity projection of the third fluorescent channel.

microglia_dna_damage

Python script to analyze DNA damage in microglial cells

napari-training-course

Lectures for a napari training course

neubias_academy_biapy

NEUBIAS Academy @Home: Interactive Bioimage Analysis with Python and Jupyter

nuclear_translocation_2d

Measuring intensity of two marker proteins inside the nucleus

nuclear_translocation_3d

Checking nuclear translocation of proteins using Voronoi-Otsu labeling and label erosion from pyclesperanto

pdac_organoids_caspase

python-for-bioimage-analysis-rms-daim

This is the repository for a Python bioimage analysis course which establishes the fundamentals of image analysis in the context of biological imaging.

rnaseq-tpm-plotter

Collection of scripts to plot TPMs (Transcripts per Million) gene expression data from .csv RNASeq-derived files. Optimized for Google Collab.

tutorial-scipy2021-bioimage-analysis-fundamentals

Tutorial for SciPy 2021 Bioimage Analysis Fundamentals in Python

unet_semseg_healthy_tumor_srs

Semantic segmentation of healthy vs tumor tissue in mouse intestinal swiss rolls

workshop-spatial-nbisweden