volker-baecker Goto Github PK

adbiasws-ilastik

Singularity Image for Ilastik for the Advanced BioImage Analysis Workshop

biaflows-jupyter

Use the biaflows software to run and benchmark image-analysis-workflows from jupyter.

coloc

docker

fiji-base

Base docker image containig fiji. To be used to create docker-images containing image analysis workflows.

game-of-life

Demo application for the 'Jenkins: The Definitive Guide' book

hello_github

a test for learning to use github

icy-headful

A docker image to run the image analysis software icy in an x-environment, so that the grphical user interface can be used.

icy-kernel

Icy kernel module

ijsegmentclusterednuclei

Segment clustered nuclei using a laplacian filter, thresholding and a binary watershed transform

ilastik-training

dockerfile to build a docker image for ilastik

imagej

Open source scientific multidimensional image processing

imagej.github.io

The ImageJ wiki

imagej_macros_and_scripts

ImageJ macros and scripts written at the imaging facility MRI

jupyter-workshop-mifobio-2018

Material for the jupyter notebook workshop at mifobio 2018

mandelbrot

markdown-two-column-documentation-example

Responsive, Two Column Documentation Layout With Markdown and CSS

microscope-metrics

mina

MiNA (Mitochondrial Network Analysis) is a project aimed at making the analysis and characterization of mitochondrial network morphology more accurate, faster, and objective. This project currently consists of a set of Python scripts (and JAVA for the user interface) for the Fiji distribution of ImageJ.

model-training

GBI/ELIXIR/EuBI/NEUBIAS hackathon model case

napari

napari: a fast, interactive, multi-dimensional image viewer for python

openmicroscopy

OME (Open Microscopy Environment) develops open-source software and data format standards for the storage and manipulation of biological light microscopy data. A joint project between universities, research establishments and industry in Europe and the USA, OME has over 20 active researchers with strong links to the microscopy community. Funded by private and public research grants, OME has been a major force on the international microscopy stage since 2000.

separate-nuclei

Docker image with FIJI and a headless imageJ macro to analyze clustered nuclei.

training-notebooks

A set of Python Notebooks to demonstrate how to access the images and metadata from OMERO

vocabularpy

w_nuclei_seg_ij_seeded_watershed

Workflow for nuclei segmentation/counting. To be used with BIAFLOWS

w_nucleitracking-imagej

Track nuclei in a time-series using ImageJ. The algorithm does a 3D segmentation of the objects to accomplish the tracking.

w_spotdetection3d-bigfish

A 3D spot detection workflow using fishquant2/BigFISH

w_spotdetection3d-ij-tophat

A BIAFLOWS workflow for 3D spot detection

wf-ntpv2.0

Wide field-nematode tracking platform