ImageJ Macros

MosaicExplorerJ

Component
Description

It stitches 3D tiles from terabyte-size microscopy datasets. Stitching does not require any prior information on the actual positions of the tiles, sample fiducials, or conversion of raw TIFF images, and the stitched images can be explored instantly.

MosaicExplorerJ was specifically designed to process lightsheet microscopy datasets from optically cleared samples. It can handle multiple fluorescence channels, dual-side lightsheet illumination and dual-side camera detection.

has topic
Light-sheet microscopy
has function
Data handling
Image stitching

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

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

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