Supplementary Information S1 Traditional insect
Contents
1. Lyons A Taylor R 2005 3D S O M A commercial software solution to 3D scanning Graphical Models 67 476 495 Agisoft 2013 Agisoft PhotoScan URL http www agisoft ru Snavely N 2010 Bundler Structure from Motion SfM for Unordered Image Collections URL http www cs cornell edu snavely bundler Furukawa Y 2010 Patch based Multi view Stereo Software URL http www di ens fr pmvs 9 10 11 12 Forbes K 2009 Visual Hulls from Uncalibrated Snapshots URL http www dip ee uct ac za kforbes DoubleMirror DoubleMirror html GigaPan Systems 2013 The GigaPan Store Products software and accessories to create gi gapixel panoramas URL http gigapan com cms shop store McHugh S 2013 Macro extension tubes and close up lenses URL cambridgeincolour com tutorials macro extension tubes closeup htm JVC Technology 2013 Viltrox JY 670 macro ring lite URL http www viltrox com en Products flashlight 2012 1121 2 html 13 Innovatronix Inc 2013 Tronix SpeedFire URL http www innovatronix com index php roducts item 35 tronix speedfire 14 Cognisys Inc 2013 StackShot Focus stacking macro rail URL http www cognisys inc com stackshot stackshot php 15 16 17 Frenergy Magnets 2013 18 Bunnings 2013 Metalmate RCR 25 4 x 254 x 1 2mm minium Square Box Tube URL http www bunnings com au metalmate rcr 25 4 x 25 4 x 1 2mm 1m aluminium square box t2. a Tronix SpeedFire flash power supply is used for fast flash charging e A StackShot macro rail 14l This device enables us to capture high magnification partially focused images at predetermined depth intervals with high position accuracy This macro rail can run automatically to capture images along a single direction The process of movement and image acquisition using macro rail starts with a press of Up button on the rail s control panel To synchronize StackShot macro rail and GigaPan robot we built a circuit interface shown in Figure 2 to convert the robot s trigger signal to a press button effect The step size of the rail is set to be approximately 70 of the depth of field of the macro lens to allow for adjacent overlapping required for stacking multi focus images e Two 1mW laser pointers for specimen alignment The laser beams are used to locate the specimen at the center of rotation of the two axis turntable so that the specimen stays at the same position while being rotated and imaged e Aluminium frames to hold the turntable laser pointers camera and macro rails in position e Button magnets 17 plastic spacers 18 epoxy glue and pins to mount insect specimens The system does not need any special software for acquiring images The EOS Utility software accompanying the camera is needed to remote tether the camera and transfer images to a computer during image acquisition Based on 2013 prices we estimat
3. Supplementary Information S1 Traditional insect mounting Figure 1 shows insects mounted horizontally with a pin going through the body from the back This mounting technique gives a strong hold on the insect body and facilitate specimen handling but provides limited access for 3D scanning Image processing and 3D reconstruction software Software used for image processing and 3D reconstruction are e Helicon Focus for multi focus image stacking to extend depth of field There are alternative open source software such as CombineZP 2 and Huggins amp Enfuse B However we found Helicon easier to use and able to exploit multi core processing e 3DSOM software 4 for 3D reconstruction from multiple view images based on visual hull tech nique The 3D reconstruction pipeline used by 3DSOM is described in 5 There are other 3D reconstruction software including commercial software Agisoft Photo Scan 6 and open source softwares Bundler 7 and Patch based Multi view Stereo mB and visual hull mesh software 9 These two off the shelf software packages together cost around AUD1700 based on 2018 prices Image acquisition equipment We use the following off the shelf components e A GigaPan Panorama Robot EPIC 100 o Normally this device is used to control the tilt and pan of a camera to capture panorama images In this project we turn it side ways and use it as a two axis turntable to control the tilt and pan of the specimen
4. e the total hardware to cost around AUD3200 to AUD5600 Examples of actual acquisition setups are shown in Figure 3 Estimation of processing time The reconstruction process described in this paper is a proof of concept and not yet optimized for speed and for large scale digitization A time estimation for each stage of the 3D reconstruction procedure for the insects shown in paper is provided in Table i The longhorn beetle Christmas beetle and Amycterine ground weevil take relatively similar amount of time to obtain a 3D model The sand wasp has increased reconstruction time due to the extra time required to manually correct the errors of background removal around the wings and to refine camera pose during reconstruction hairs significantly increase the time for pose refinement The granary weevil due to its small size takes much more time to mount using a microscope acquire multi focus images and perform 3D reconstruction It is often the case that the reconstruction stage is repeated several times to find and fix errors in background removal or to iterate the refinement process until the result is acceptable Therefore the times provided in Table 1 should only be considered as indicative Informal feedback on using a 3D insect model for species identi fication One possible use case for 3D insect models is species identification In drafting this paper we needed to fully identify the Christmas beetle We asked CSIRO entomologist Mr To
5. m Weir to try to do so from the photograph the 3D model and finally the actual specimen In addition to identifying the specimen as a male Anoplognathus viriditarsus from the 3D model alone Mr Weir provided feedback which we summarize as e The single top view photograph does not capture the key features needed to identify the species just enough information to determine its genus The features are located at different parts of the insects such as abdomen head mouth claws rear end etc Multiple images captured at particular angles are required to show all these features The 3D model provides useful extra information and allows views from any angle There are still missing features such as the mouth area and hairy surface on the head nose due to resolution of geometries and texture colours However the available features are roughly enough to identify its species Examination and species identification would be facilitated if the texture information was provided more clearly or high resolution images of the features were attached to the model The actual specimen obviously provides all the information needed but needs examination under a microscope for some features such as the mouth area and hair surface on the head However out of focus effect and other physical restrictions makes the use of microscope to view the actual specimen more cumbersome than to view the 3D model of specimen on a mobile device such as iPad Identification invol
6. rol box to accept external trigger A Circuit diagram to provide interface between trigger output of GigaPan robot and StackShot control box The resistor and the opto coupler convert the trigger signal to a press button action B the resistor and opto coupler are soldered to a connector which can be mounted to the case of the control box C Finished the control box with the extra input connector on the left Note that the connector pins of GigaPan trigger cable have to be swapped such that red cable goes to position 2 and white cable to position 3 Figure 3 Examples of actual set up in normal mode A and macro mode B The GigaPan Panorama Robot is mounted sideways to act as a two axis turntable The camera is turned 90 around optical axis so that it can capture images that better fit the specimen and the mat target Video of the system B at work are available at 19
7. to be imaged The GigaPan Panorama Robot connects to a camera via a cable and triggers a camera to capture one or more images per rotation angle e A Canon 600D camera or better It provides low noise high resolution images 18MP It is highly customizable with several ports for external trigger input flash trigger output and a USB port for remote tethering One problem with many DSLR cameras is that they rely on a mechanical shutter which can cause mechanical vibration and image blur The image blur due to mechanical shutter vibration can be alleviated by using a camera flash triggered between shutter movement e A Canon EF 100mm macro lens for normal mode and Canon MP 65mm for macro mode The EF 100mm lens provides magnification of 1x or smaller while the MP E 65mm lens provides magnification from 1x to 5x These macro lenses also have much less optical distortion than some other lenses A low cost solution to make normal lens achieve higher magnification is to add a macro extension tube between the camera and the lens However this often increases optical distortions 1 The depth of field of MP 65mm lens as function of magnification and aperture can be obtained from its user manual e A Viltrox JY 670 macro ring flash 2 This flash provides illumination and reduces exposure time Short exposure time is critical for macro photography to reduce image blurring due to vibration from the camera s mechanical shutter Additionally
8. ube_p1067815 19 Nguyen C Adcock M Lovell D Mantle B La Salle J 2014 doi 10 4225 08 531FE0104C11A URL Dick Smith 2013 Figure Legends Keychain 1mW Laser Pointer office accessories keychain 1mw laser pointer dsau xp0671 Bunnings 2013 Castor Cup Round Tic 48mm Clear Plastic 25685 URL com au castor cup round tic 48mm clear plastic 25685_p4050109 URL Neodymium Disc Magnet 10mm dia x 3mm height N50 URL wiw frenergy com au products Disc 10mm dia x 3mm height N50 htm1 Tables Table 1 Time consumption estimation Insect Mounting min Acquisition min Reconstruction min Longhorn beetle 5 15 60 Christmas beetle and ground weevil Sand Wasp 5 15 120 Granary Weevil 30 180 120 http www dicksmith com au http www bunnings Insect collections going 3D http dx doi org 10 4225 08 531FE0104C11A able at http www youtube com watch v THvfu6shJj g amp list UUak3NZxjNnWip327vYL8RLA or http publish viostream com play xbz189zsuhn8 Figure 1 Traditional insect mounting A metal pin pierces the body of an insect from the back providing stronghold to the specimen However this mounting can be inconvenient for 3D scanning due to the speciment s horizontal body axis GigaPan A EPIC 100 Trigger Out 4N25 5 connect to Up button 4 of StackShot Up e O Down Config Figure 2 Modification of StackShot macro rail s cont
9. ves matching the given specimen to its corresponding specimen in the Australian National Insect Collection and comparing it to closely related species For identification purposes the natural colour 3D model is much more helpful than the Micro CT 3D model The better geometry accuracy of the Micro CT model does not assist in this instance Higher resolution of the natural colour 3D model is desirable to provide details of key identification features This is particularly important for features such as hairs that never get included in the 3D models One solution would be to attach high resolution photographs to locations of the key features To make the 3D model useful for species identification it is important to know in advance all key features and the identification procedure and level Ideally this information would be arranged in a way that directly supports fast correct identification 3D visualization and annotation could make the identification procedure more obvious that the instructions currently provided in text and 2D illustrations References 1 HeliconSoft 2013 Helicon Focus URL http www heliconsoft com heliconsoft products helicon focus Hadley A 2010 CombineZP URL http www hadleyweb pwp blueyonder co uk CZP News htm D Angelo P 2013 Hugin amp Enfuse URL http hugin sourceforge net tutorials index Creative Dimension Software Ltd 2013 3DSOM URL http www 3dsom com Baumberg A
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