Workflow

A workflow is a set of components assembled in some specific order to

  1. Measure and estimate some numerical parameters of the biological system or
  2. Visualization

for addressing a biological question. Workflows can be a combination of components from the same or different software packages using several scripts and manual steps.

Description

MiNA is a simplified workflow for analyzing mitochondrial morphology using fluorescence images or 3D stacks in Fiji. The workflow makes use of ImageJ Ops3D ViewerSkeletonize (2D/3D)Analyze Skeleton, and Ridge Detection. In short, the tool estimates mitochondrial footprint (or volume) from a binarized copy of the image as well as the lengths of mitochondrial structures using a topological skeleton. The values are reported in a table and overlays (or a 3D rendering) are generated to assess the accuracy of the analysis.

example skeleton image (from https://imagej.net/plugins/mina#processing-pipeline-and-usage)

GPU-Accelerating ImageJ Macro Image Processing Workflows Using CLIJ

Submitted by czhang on Thu, 04/27/2023 - 09:55

This chapter is part of this book. The chapter introduces GPU-accelerated image processing in ImageJ/Fiji. The reader is expected to have some pre-existing knowledge of ImageJ Macro programming. Core concepts such as variables, for-loops, and functions are essential. The chapter provides basic guidelines for improved performance in typical image processing workflows.

Description

The authors present an ImageJ-based, semi-automated phagocytosis workflow to rapidly quantitate three distinct stages during the early engulfment of opsonized beads.

Description

Junction Mapper is a semi-automated software (Java Desktop application) for analysing data from images of cells in close proximity to each other in monolayers. The focus of Junction Mapper is to measure the morphology of cell boundaries, define single junctions and quantify the length, area and intensity of the staining of different proteins localised at cell-cell contacts. The output are various unique parameters that assess the contacting interface between cells and up to two junctional markers.

junction mapper