SHORT COURSE on FOCUS STACKING & PHOTOGRAMMETRY

Abstract

Focus stacking and 3D modeling workstations are rising in popularity to document scientific observations but, few systems can output high quality imagery and 3D models for a wide range of interdisciplinary sample sizes with variable characteristics.  We aim to use the Macropod PRO 3D by Macroscopic Solutions to methodically combine focus stacking and photogrammetry techniques to generate high quality 3D models of specimens Apis mellifera and Halictus tripartitus.

Apis mellifera is a moderately sized specimen with high contrasting features and Halictus tripartitus is a small sized specimen with moderately reflective features.  The two specimens will serve as examples to define a repeatable method for imaging technicians to create 3D models using photogrammetry from focus stacked imagery. The content for each sample will be presented side-by-side in an instructive format featuring an introduction and 10 lessons.

The course will be a resource to participants in Extending Research through Image and Trait Digitization (Big-Bee), which is a US National Science Foundation funded project to advance the digitization of biodiversity collections.

Big-Bee prompted five key and important innovations, two related to hardware and three related to workflow efficiency. Innovative solutions relating to hardware are designed to consistently illuminate specimens with minimal to no anomalies between shots (i.e., glare, reflection, oversaturation, poor contrast) and the option to easily orient specimens in a gimbal-like fashion to mount specimens quickly and efficiently. The images are focus stacked in Zerene Stacker and 3D models are generated in Agisoft Metashape.

Introduction and Overview

Macropod PRO 3D

The Macropod Pro 3D uses a motorized linear stage and rotary stage that automatically moves the specimen relative to the camera, lens, and lighting apparatus. The specimen is photographed and illuminated from back to front using the linear stage to record thin and overlapping focal sections used to generate a final focus stacked image of the specimen. Images are captured using a speed light flash and open aperture to physically produce the sharpest image possible of each individual focal plane. This process is repeated as the rotary stage rotates the specimen around a vertical axis perpendicular to the lens in 2-degree intervals along two opposing 235-degree arcs. In this example, the process is repeated 235 times.

Zerene Stacker discards blurry areas of each image and combines each focal section to create an output image that is completely in focus; hence the term, focus stacking. A folder splitter automatically separates pre-focus stacked images into 235 unique folders and a batch processer automatically focus stacks all 235 perspectives. The result is 235 high-resolution, color-accurate images captured concentrically around the specimen comprising the adequate dataset required for photogrammetry.

Agisoft Metashape analyzes and aligns all 235 images and virtually places them into the exact position relative to the specimen from where they were captured. The methods used to align these photos can sometimes vary; however, subsequent steps remain the same. The software creates a 3D model by triangulating tie points identified from changing perspectives from adjacent source imagery. The color profiles from each source image are matched and combined to render the external texture resulting in a highly detailed volumetric model of any specimen >50 microns in size.

Sample Preparation

 

Stage Selection

 

Lens Selection

 

Camera Selection

 

Before we Begin


Lesson 1: Equipment & Lighting Set-Up

Lesson 2: Image Capture

Lesson 3: Batch Focus Stacking

Lesson 4: Batch Editing

Lesson 5: Masking

Lesson 6: Image Aligning

Lesson 7: Mesh Building

Lesson 8: Texture Building

Lesson 9: Scale Bar

 

Lesson 10: File Saving and Output