Volker's repositories
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
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.
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.github.io
The ImageJ wiki
markdown-two-column-documentation-example
Responsive, Two Column Documentation Layout With Markdown and CSS
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
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
W_VOLKER_MIFOBIO_EXAMPLE_SEG
An example workflows to demonstrate adding workflows to BIAFLOWS
WF-NTPv2.0
Wide field-nematode tracking platform