ImageJ Macros

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

Customizing ImageJ

These slides give an introduction to user interfacre customization in ImageJ using ImageJ Macro and to ImageJ Macro Markdown.

Big thanks to Jerome Mutterer (IBMP) and Nicolas De Francesco (IMBICE) who shared material openly I reused when making these slides.

Supplementary material is available as well under this doi: 10.5281/zenodo.4561714

NDPI Export Regions Tool

Workflow
Description

The tool exports rectangular regions, defined with the NDP.view 2 software (hammatsu) from the highest resolution version of the ndpi-images and saves them as tif-files.

Click the button and select the input folder. The input folder must contain pairs of ndpi and ndpa files. The regions will be exported to a subfolder of the input folder names zones.

has topic
Digital histology
has function
Data handling
imagej toolset to export regions from ndpi and ndpa-files

Analyze Spheroid Cell Invasion In 3D Matrix

Workflow
Description

The tool allows to measure the area of the invading spheroïd in a 3D cell invasion assay. It can also count and measure the area of the nuclei within the spheroïd.

has topic
Live sample imaging
Widefield microscopy
Fluorescence microscopy
has function
Cell segmentation
Object counting
need a thumbnail
Subscribe to ImageJ Macros