Component

Component

A Component is an implementation of certain image processing / analysis algorithms.

Each component alone does not solve a Bioimage Analysis problem.

These problems can be addressed by combining such components into workflows.

Description

Local Z Projector is an ImageJ2 plugin, available in Fiji, that can perform local-Z projection of a 3D stack, possibly over time, possibly very large.

LZP performs projection of a surface of interest on a 2D plane from a 3D image. It is a simple tool that focuses on usability and is designed to be adaptable to many different use cases and image quality.

  • It can work with 3D movies over time with multiple channels.
  • It can work with images much larger than available RAM out of the box.
  • It takes advantage of computers with multiple cores, and can be used in scripts.

 

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Viv

Description

Viv is a JavaScript library providing utilities for rendering primary imaging data. Viv supports WebGL-based multi-channel rendering of both pyramidal and non-pyramidal images. The rendering components of Viv are provided as Deck.gl layers, facilitating image composition with existing layers and updating rendering properties within a reactive paradigm.

Rendering a pyramidal, multiplexed immunofluorescence OME-TIFF image of a human kidney using additive blending to render four image channels into a single RGB image in the client.
Description

TrackMate based tracker to be used when uploading integer labelled segmentation images, coming from a Deep Learning tool such as stardist. To use this tool efficiently we provide a python notebook to collect/localize the position of cells, this step creates a CSV file which can then be loaded into the Fiji tracker to do particle tracking with TrackMate interface.

Description

MSER based on implementation in imglib2 provided as an interactive GUI tool for spot detection in 2/3/4D images.

Description
Quote: >LaRoME = Label + Region Of Interest + Measure >Label image (aka Count Masks): An image in which pixels of an object have all the same value. Each object has a unique value. >Measurement image: An image in which pixels of an object have all the same value, corresponding to a measurement (Area, Angle, Mean...)
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