¶ Activating the PTBIOP Fiji update site
Our Macros and Plugins make strong use of ActionBar and sometimes ImageScience
- Go to
Help→Update... - Select
Manage Update Sitesand check the left side box for all the following sites: (Alphabelical order)
- IBMP-CNRS - ActionBar and others
- ImageScience - Laplacian Filter (It used to be bundled with Fiji, but no longer)
- PTBIOP - Our update site https://biop.epfl.ch/Fiji-Update
¶ BIOP recommended Fiji update sites
We recommend to also activate the following update sites.
- BIG-EPFL - Many tools for image processing by the http://bigwww.epfl.ch/
- CSBDeep - TensorFlow for Java, necessary for StarDist https://csbdeep.bioimagecomputing.com/
- OMERO 5.5-5.6 - OMERO library for data management https://www.openmicroscopy.org/omero/
- StarDist - Deep learning model for nuclear detection https://github.com/stardist/stardist
- TrackMate-StarDist - Using StarDist models in TrackMate https://imagej.net/plugins/trackmate/detectors/trackmate-stardist
¶ PTBIOP Update site contents
Here is a list of all the plugins and tools that we bundle in our update site
| Tool | Description | Link |
|---|---|---|
| Cellpose Wrapper | To use Cellpose 2D/3D in Fiji | https://github.com/BIOP/ijl-utilities-wrappers |
| StarDist Wrapper | To use StarDist 2D/3D in Fiji | https://github.com/BIOP/ijl-utilities-wrappers |
| BDV Playground | Tools to increase the functionality of BigDataViewer | https://github.com/bigdataviewer/bigdataviewer-playground |
| Devils | Non linear visual display adjustment for high dynamic range images | https://github.com/BIOP/ijp-DEVILS |
| ABBA | Aligning Big Brains and Atlases: 2D to 3D Atlas registration | https://github.com/BIOP/ijp-imagetoatlas |
| Operetta Importer | API for communicating with and exporting PerkinElmer Operetta datasets | https://github.com/BIOP/ijp-operetta-importer |
| BIOP LUTs | A collection of Lookup Tables used at the BIOP | https://imagej.net/plugins/biop-lookup-tables |
| BIOP Basics | ActionBar to help batch process scripts | https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/imagej_tools/biop-basics/ |
| BIOP Channel Tools | ActionBar to set channel colors, Ranges, LUTs and montage options | https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/imagej_tools/ijab-biop_channel_tools/ |
| BIOP Common Tools | ActionBar with shortcuts to common actions in Fiji | |
| BIOP MultiManual Select | ActionBar to simplify manual ROI creation and saving in Fiji | |
| BIOPLib | A small library of convenient macro functions | |
| FRC | Fourier Ring Correlation plugin implementation | https://github.com/BIOP/ijp-frc |
| LaRoMe | Label Image to ROI Converter | https://github.com/BIOP/ijp-LaRoMe |
| Multi Stack Montage | Allows stacks to be montaged as well | https://imagej.net/plugins/multi-stack-montage |
| JACoP-B | Adds extra functionality to the already great JACoP plugin | https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/imagej_tools/jacop_b/ |
| Max Inscribed Circles | Circle packing for ROIs. Includes "Spine" detector | https://imagej.net/plugins/max-inscribed-circles |
| Auto Color Balance | Simple tool for auto-white balancing RGB images | |
| Simple Color Balance | Color balance via a background ROI selection for RGB images | |
| Cell Maker | Small script to expand rois into cells using distance maps and voronoi diagrams | |
| Linear Unmixing | Allow to calculate and apply simple linear unmixing matrices | |
| Upload to OMERO | Script for converting and uploading images to OMERO |