✒ Fiji ROI Editor 1.0

Fiji ROI Editor 1.0 can run as a Fiji plugin or as a standalone Jython application. Fiji ROI Editor 1.0 facilitates managing, editing, and analyzing Regions of Interest (ROIs) in image data. This Fiji Roi Editor is a derailed modification of the Fiji plug in LabelsToRois. The Fiji Roi Editor is implemented in Jython or Java-Python. The goal of RoiEditor is to remove “bad ROIs” from microscope images and to generate the data to perform statistics on the basic ROI properties: area and the Feret-parameters. Fiji ROI Editor 1.0 has extended editing capabilities, but lacks the erosion and multiple slice functionality of the Fiji plugin LabelsToRois. Fiji RoiEditor cannot segment ROIs in photographs. cellpose is used for that purpose.

A standalone CPython-based twin of the Fiji RoiEditor, RoiEditor 2.0, is available too on GitHub

✨ Features

• The original photograph is loaded from a .png or .tif(f) file.
• The cellpose label-data can be read from a .png file.
• The ROIs are stored in and read back from a Fiji compatible ROI zip file.
• The measurements are collected in a dedicated class, not using Fiji's table.
• The ROIs are stored in a simple and lean TinyRoiManager.
• Contrary to most ROI-handling apps or plug ins, RoiEditor never removes ROIs from the collection: Deleted ROIs are marked, but not removed.
• The state data and other metadata is stored in a json file in the ROI zip file.
• Area & Feret measurements are computed for all ROIs, not using Fiji's measurement table.
• The stats for each measurement are shown in a histogram window.
• The user can select the edge of the ROI-cloud or the outliers for each measurement for deletion.
• An outlier for a measurement is a value outside of [q1 - 1.5 * IQR,q3 + 1.5 * IQR].
• The measurements are written to a .csv file.

Installation on Windows

• Fiji must be installed before Fiji ROI Editor 1.0 can be installed.
• After making a local copy of the repo, run install_Fiji_RoiEditor.bat This will install the Fiji ROI Editor both as a plugin and a standalone app. After installation, you can remove the folder from which you started the install.

standalone execution

• If the installation goes well, an icon appears on the desktop for the standalone execution.
• The RoiEditor can also be started by clicking start_RoiEditor.bat

Fiji plugin

• when installed 'Edit ROIs' will appear deep down on the list of plugins in the plugin dropdown.
• clicking 'Edit ROIs' will start the editor in the Fiji context.

🧮 Workflow

The plot below shows the integrated workflow using cellpose and RoiEditor.

Compared to RoiEditor 2.0 the Fiji ROI Editor 1.0 lacks the export of measurements to an xlsx file and the overlay with the ROIs colored according to their distance to to the median of the selected measurement.