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bigtiffresampler

A small C# program that can resample very large BigTiff files fast.

csbdeep

Image restoration for fluorescence microscopy

fiji

A "batteries-included" distribution of ImageJ :battery:

hrm

The Huygens Remote Manager is an open-source, efficient, multi-user web-based interface to the Huygens software by Scientific Volume Imaging for parallel batch deconvolutions.

ij-svg-roi

Class for creating imageJ ROIs from SVG paths

ijm-pts

ActionBar for PTS Analysis by the BioImgaing and Optics Platform (BIOP

ijp-biop-lib-installer

Short Plugin that allows one to load a series of ImageJ1 Macro Functions to the Macro Interpreter of a Running Fiji Library, that way these functions are accessible to all subsequently run macros.

ijs-trackmate

some groovy scripts to use TrackMate

image_expression_parser

imagej-maven-plugin

A Maven plugin to help development of ImageJ and ImageJ plugins

imagej1

Wayne Rasband's ImageJ 1.x repository, updated once a night. To develop this code, use https://github.com/imagej/ImageJA.

imaris-average-spots-by-distance

This XTension takes in a spots object and a distance value and returns a new spots object with spots closer than the given distance removed averaged to a single spot.

imglib2-introductory-workshop

ImgLib2 Introductory Workshop

libinstaller

Macro Function Library installer for Fiji/ImageJ

list-of-update-sites

The update sites ImageJ knows about automatically

localthickness

microscopy-icons

Icons describing multiple microscopy techniques, as used by https://www.epfl.ch/research/facilities/ptbiop/equipment/

minimal-ij1-plugin

A simple Maven project implementing an ImageJ 1.x plugin

morpholibj

Collection of mathematical morphology methods and plugins for ImageJ

phantast-fiji

Repository for the FIJI/ImageJ implementation of the phase contrast microscopy segmentation toolbox (PHANTAST)

scripting-groovy

JSR-223-compliant Groovy scripting plugin

swissbias.github.io

Website for the SwissBIAS network: Swiss BioImage Analysts's network

trackmate-multi-log

Some extra modules for TrackMate

tracmit

TRACMIT: Algorithm for Single cells on Micropatterns through mITosis

universalmediaserver

A DLNA-compliant UPnP Media Server.

w1-dual-z-stack

Code Written Originally for Melina Scholtze by Arne, then Oli This code when run on VisiView, allows for the user to define two different acquisition settings for the same timelapse. Eg. One Brightfield Stack acquisition of 10 planes and a step of 1um, followed by a 2 channel fluorescent acquisition with 3 planes and a step of 0.24um. Contains a simple GUI that manages to get and set laser powers and remembers previous settings.