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Regions of Interest

The ROI manager plugin lets you capture, draw, tag, and revisit regions of interest. ROIs persist across sessions and work without a cell table, so this is part of the essentials.

The plugin has two tabs: ROI browser (find and revisit ROIs) and ROI editor (capture and edit them).

Two kinds of ROI

UELer stores two different things under one name, and the difference matters when you filter or export:

  • a view ROI is a saved viewport — a bookmark of where you were looking, at what zoom, with which markers and overlays;
  • a shape ROI is a polyline or polygon you drew on the image, which also carries its geometry and a physical length.

Both live in the same table and the same browser. Everything below about tags, comments, filtering and export applies to both.

Capturing an ROI

  1. Pan and zoom the main viewer to frame the region you want.
  2. Open the ROI editor tab.
  3. Click Capture view.

The capture records the current viewport, the active FOV (or map), your marker set choice, and the current mask/annotation settings, so re-centering later can restore the same look.

Before or after capturing you can set:

  • Name: — an optional custom name for the ROI.
  • Add tag: / Tags: — free-form tags (type or pick; new tags are allowed).
  • Comment: — a free-text note.
  • Marker set: — which marker set to associate (Current set, None, or a saved set).

Use Update to save edits to the selected ROI, Delete to remove it, and Center / Center with preset to jump the viewer back to a saved ROI (the latter also re-applies the ROI's saved marker/mask/annotation presets).

Only current FOV

The editor's Only current FOV checkbox (on by default) filters the saved-ROI dropdown to the active FOV.

Drawing a shape ROI

The editor tab also has a shape block for drawing directly on the image — use it to mark a boundary, trace a structure, or measure a distance.

  1. Click Draw, then click on the image to place vertices. The summary line under the buttons tracks the shape as you go.
  2. Tick Closed shape (polygon) before finishing if you want the shape closed; leave it clear for an open polyline.
  3. Correct as you go with Undo / Redo, or abandon the whole shape with Cancel.
  4. Click Finish to end the shape, then Save shape to store it.

A saved shape is an ROI like any other: give it a Name:, Tags: and a Comment:, and it appears in the browser gallery alongside your captured views.

  • Show shapes on canvas (on by default) draws the saved shapes over the image. Untick it to get an unobstructed view without deleting anything.
  • Edit loads the selected shape ROI back into the editor so you can move or add vertices and save it again.

Shapes measure themselves

The summary line reports the shape's length in µm as well as pixels, computed from the Pixel Size (nm): value in Advanced Settings. If that value is wrong, so is the length — see Display Settings.

Browsing ROIs

The ROI browser tab shows a paged thumbnail gallery (12 per page) of your ROIs. Click a tile to jump to that ROI; with Apply saved preset on click enabled, clicking also restores the ROI's saved presets.

Filter the gallery with:

  • Tags: and a Tag logic toggle — All tags (AND) or Any tag (OR).
  • FOVs: — restrict to specific FOVs.
  • Only current FOV — restrict to the active FOV (off by default here).

The browser has simple and advanced filter sub-tabs. The advanced tab is an expression editor:

Expression-based selection

In the advanced sub-tab, build a boolean tag expression using &, |, !, and parentheses — for example:

(good & figure1) & !excluded

Insert operators and tag names with the provided buttons, then click Apply. Leave the expression blank to fall back to the simple tag filter.

Where ROIs are stored

ROIs are saved to:

<base_folder>/.UELer/roi_manager.csv

You can also Export / Import the ROI table from the editor tab (paths are resolved relative to the base folder).

ROIs and Map Mode

ROIs captured in map mode are stored with an empty fov and a populated map_id, and are shown with a [MAP:<id>] location label. The FOV-scope filters are disabled while map mode is active.

Exporting ROI images

To render ROIs to image files (single-FOV or map-mode), use the Batch Export plugin's ROIs tab.