imagejan
Bio-Image Analyst / Image Data Scientist in the Facility for Advanced Imaging and Microscopy at FMI Basel
Friedrich Miescher Institute for Biomedical Research (FMI)Basel, Switzerland
Pinned Repositories
imagej-plugins-batch
Batch Processor Plugins for ImageJ
angiotool
A trial to convert AngioTool ( https://ccrod.cancer.gov/confluence/display/ROB2/Home ) into a Fiji plugin
BigTrace
FIJI plugin for tracing of curvilinear structures in volumetric microscopy datasets
blind-experiment
An ImageJ plugin to assist with blind analysis of image data.
image-processing-courses
batch-processor
A Batch Processor for SciJava
scijava-common
A plugin framework and application container with built-in extensibility mechanism :electric_plug:
imagejan's Repositories
imagejan/BigTrace
FIJI plugin for tracing of curvilinear structures in volumetric microscopy datasets
imagejan/bioimagebook.github.io
An introduction to bioimage analysis - http://bioimagebook.github.io
imagejan/DeformingMesh3D-plugin
An imagej/fiji plugin for interactive segmentation of 3D
imagejan/ACSAuto
ACSAuto script to semi-automatically evaluate ultrasound pictures
imagejan/betaseg.github.io
imagejan/biojava
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
imagejan/ez_zarr
GIve easy, high-level access to ome-zarr fileset
imagejan/faim-ipa-feedstock
A conda-smithy repository for faim-ipa.
imagejan/faim-jetraw-playground
imagejan/FunctionFit
Extension of Saalfelds mpi-cbg package for function fits
imagejan/imagej-plugins
A collection of ImageJ plugins
imagejan/imagejan
imagejan/insolitum
imagejan/labkit-command-line
Labkit Command Line - Segment huge images on a cluster
imagejan/labkit-pixel-classification
imagejan/labkit-ui
Advanced Tool for Labeling And Segmentation
imagejan/magicgui
build GUIs from type annotations
imagejan/mastodon
Mastodon – a large-scale tracking and track-editing framework for large, multi-view images.
imagejan/measures
Java implementation of measures for quantitative evaluation of biomedical tracking in general.
imagejan/mobie-utils-python
Python tools for MoBIE
imagejan/mobie-viewer-fiji
imagejan/mobie.github.io
imagejan/MorphoLibJ
Collection of mathematical morphology methods and plugins for ImageJ
imagejan/nbdev
Create delightful software with Jupyter Notebooks
imagejan/ngff
Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
imagejan/prefect-shell
Prefect tasks and subflows for interacting with shell commands.
imagejan/render-python
A python interface for render
imagejan/scikit-image
Image processing in Python
imagejan/sciview-update-sites
The buttercup update site for sciview
imagejan/WIPP
Web Image Processing Pipeline (WIPP)