martinschatz-cz
BioImage Analyst
UCT Prague, VMCF - Science Faculty of Charles University, Natinal Technical Library in PraguePrague, Czech republic
Pinned Repositories
bia-overview
Jupyter-book repo for overview of my fav. sources and tools for BiA
binder-demo1
Simple tutorial example of binder enabled demo with trivial calcuation
example_pytest
genotoxicity-bia
ImageJ_Pneumonia_Estimation_Tool
ImageJ tool for estimation of pneumonia in CT images (of lungs)
pyimagej-julab
Playground for testing PyImageJ with Jupyetr Lab
SciAugment
SciAugment aims to provide tools for image augmentation based on machine on which images were taken.
SciCount
SciCount is tool focused on counting and classifying of objects in image-like data and scientific images, with training and example datasets.
testovaci
test repo
the-segmentation-game
Gamified image segmentation quality estimation
martinschatz-cz's Repositories
martinschatz-cz/SciAugment
SciAugment aims to provide tools for image augmentation based on machine on which images were taken.
martinschatz-cz/bia-overview
Jupyter-book repo for overview of my fav. sources and tools for BiA
martinschatz-cz/openAI_speech_transcript
Example of using openAI to transcript a mp4 record of 'Data Stewardship Course for Doctoral Candidates' presentation
martinschatz-cz/genotoxicity-bia
martinschatz-cz/bia-bob
BIA Bob is a Jupyter+chatGPT/Gemini-based assistant for interacting with image data and for working on Bio-image Analysis tasks.
martinschatz-cz/BioImage-Analysis-and-Data-Processing-Workshop-2024
This repository hosts material for the BioImage Analysis and Data Processing Workshop 2024, which takes place in VMCF Microscopy Facility, Vinicna 7, Prague, Czechia
martinschatz-cz/cell_interaction_gnn
martinschatz-cz/circleci_LLMOps
martinschatz-cz/cp-convert
martinschatz-cz/CZI_processing
CZI files processing notebooks
martinschatz-cz/docker-ci-automation
GitHub Actions automation examples with Docker's official actions
martinschatz-cz/docker-example-omero-microservices
Example of running OMERO.server microservices
martinschatz-cz/docker-jupyter_lab
martinschatz-cz/Docker-Tools
docker tools and examples
martinschatz-cz/docker_parallel_processing
parallel procesing using Python script
martinschatz-cz/docker_python39_template
docker python 3.9 simple app run template
martinschatz-cz/EMBL-Granulometry_image-analysis-practical-2023
EMBL-Granulometry
martinschatz-cz/fair-python-cookiecutter
An opinionated cookiecutter template to kickstart a modern best-practice Python project with FAIR metadata.
martinschatz-cz/GitLab-on-Docker
gitlab with docker and local logs
martinschatz-cz/jupyter_book_template
Jupyter Book cookiecutter template with CI
martinschatz-cz/Lecture-materials
deeplife4eu materials
martinschatz-cz/llm_function_generator
martinschatz-cz/martinschatz-cz.github.io
martinschatz-cz/ND2_processing
martinschatz-cz/rdmkit
ELIXIR Data Management Toolkit - Find the answers to your research data management questions here.
martinschatz-cz/schemastore
A collection of JSON schema files including full API
martinschatz-cz/Survey_2024
Analysis of 2024 Survey Results
martinschatz-cz/udemy-docker-mastery
Docker Mastery Udemy course to build, compose, deploy, and manage containers from local development to high-availability in the cloud
martinschatz-cz/YOLOBee
martinschatz-cz/yolov5_local_base