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.

Nuclei Segmentation (Cellpose)

Workflow
Description

This workflow processes a group of images containing cells with discernible nuclei and segments the nuclei and outputs a binary mask that show where nuclei were detected. It performs 2D nuclei segmentation using pre-trained nuclei segmentation models of Cellpose. And it was developed as a test workflow for Neubias BIAFLOWS Benchmarking tool.

has topic
Machine learning
has function
Cell segmentation
need a thumbnail

MiNA - Mitochondrial Network Analysis

Workflow
Description

MiNA is a simplified workflow for analyzing mitochondrial morphology using fluorescence images or 3D stacks in Fiji. The workflow makes use of ImageJ Ops, 3D Viewer, Skeletonize (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.

has topic
Bioimage informatics
Fluorescence microscopy
has function
Image analysis
Image thresholding
Morphological operation
Skeletonisation
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.

Semi-automated quantification of three stages of phagocytosi using ImageJ

Workflow
Description

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

has topic
Fluorescence microscopy
Bright field microscopy
has function
Cell segmentation
Interactive segmentation
Object classification
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