Creating a 3D HREM Reconstruction of a Mouse Embryonic Heart in Dragonfly

ashley7671
Nov 17
2 min read

High-Resolution Episcopic Microscopy (HREM) is a powerful technique for generating high-contrast, isotropic 3D datasets. In this tutorial, we’ll walk through how to transform an HREM image stack of a mouse embryonic heart into a polished 3D reconstruction using Dragonfly. We’ll cover importing data, setting voxel size, basic rendering and exporting a cinematic flythrough. All screenshots are captured from our workflow using Indigo Scientific’s HREM system.

What you’ll need

Dragonfly (any recent version with volume rendering & movie tools)
An HREM image stack (TIFF/PNG sequence)
Basic familiarity with Dragonfly’s workspace

Step 1: Open Dragonfly & get oriented

Familiarize yourself with the Project pane, Workspace, and Properties/Inspector areas. We’ll use these throughout.

Step 2: Import the HREM image stack

Go to File → Import → Image Sequence. Ensure the sequence order is correct (ascending slice index).

Select Open Folder.. and navigate to the image stack

Select Next >

Tip: If your stack is inverted/monochrome in an unexpected way, toggle the reader options for bit depth, endianness, and grayscale interpretation.

Step 3: Set voxel size (scale calibration)

Set correct voxel size in X/Y/Z to preserve proportions in 3D. This comes from your acquisition metadata (e.g., microns per pixel and section thickness). Once complete click 'Finish'.

Why it matters: Accurate voxel spacing ensures the heart’s anatomy isn’t warped and that measurements are meaningful.

Step 4: Adjust brightness/contrast (window/level)

When we have the model in dragonfly it often doesn't start out how we need it so we can adjust some parameters to fix this. Feel free to adjust to you’re preference!

Use the Histogram/Window controls to balance contrast. HREM typically benefits from a slightly narrower window to emphasize tissue boundaries.

Go to Scene View Properties and uncheck Use lighting
Set all upper settings as highlighted

Go to the Window/Levelling toolbar and select Colour mapping to be between the two points (the second option)
Adjust the points in the histogram window using the yellow handles, moving them left and right, to remove all background but not the features

Pro tip: Keep an eye on clipping—avoid truncating bright features.