Virtual Orientation Tools (VOTj): Fiji plugins for object centering and alignment

TL;DR

This paper introduces VOTj, a set of Fiji plugins that help standardize images by centering and aligning objects to a common orientation.

Contribution

The novel contribution is the development of interactive and batch-compatible Fiji plugins for object alignment using PCA.

Findings

VOTj uses PCA to determine and align object orientation in images.

The plugins support multi-dimensional images and can be used in custom workflows.

They allow interactive alignment and batch processing of image directories.

Abstract

Standardizing image datasets is essential for facilitating overall visual comparisons and enhancing compatibility with image-processing workflows. One way to achieve homogeneity for images containing a single object is to align the object to a common orientation. Here, we propose the Virtual Orientation Tools (VOTj): a set of Fiji plugins to center and align an object of interest in images to a vertical or horizontal orientation. To process an image, the plugin requires either a mask outlining the object or a rough annotation of the object directly drawn by the user in the image. The current object orientation is retrieved using Principal Component Analysis (PCA), from which the optimal alignment is derived. The plugins support multi-dimensional images to allow, e.g., aligning individual time points of a time-lapse. The tools can be used for a variety of samples and imaging modalities. Besides, the plugins enable the interactive alignment of a list of images from a directory for batch execution and can be included in custom image-processing workflows using macro-recording.

Figures