Production of 3D Printed Scale Models from Microscope Volume Datasets for use in STEM Education

Abstract

Understanding the three-dimensional morphology of a biological sample at the microscopic level is a prerequisite to a functional understanding of cell biology, tissue development and growth. Images of microscopic samples obtained by compound light microscopy are customarily recorded and represented in two dimensions from a single orientation making it difficult to extrapolate 3D context from the 2D information. The commercialisation of fast, laser-based microscope systems (e.g. confo-cal, multi-photon or lightsheet microscopy) capable of generating volume datasets of microscopic samples through optical sectioning, coupled with advances in computer technology allowing accurate volume rendering of these datasets, have facilitated significant improvement in our 3D understanding of the microscopic world in virtual space. The advent of affordable 3D printing technology now offers the prospect of generating morphologically accurate, physical models from these microscope volume datasets for use in science education, outreach and engagement. 3D printed scale replicas will provide improved sensory perception, offering tactile as well as visual interaction, leading to improved understanding of structure function relationships. Here we present a technique to reliably generate detailed, physical 3D models from Z-stacks of optical sections from confocal and lightsheet microscopes using affordable , entry-level 3D printing technology. We use the technique to generate 3D printed models of a variety of different biological samples at a range of scales including pollen grains from two species of plant; blood cells from both human and earthworm species, a section of plant root; the compound eye of an ant; and a developing Ze-brafish larva; all of which have been used in our teaching, engagement and outreach activities. Our methods can, in principle, be used to generate 3D printed models from microscope volume datasets of any small fluorescent or reflective samples.

Full text

Production of 3D Printed Scale Models from Microscope
Volume Datasets for use in STEM Education
Perry I1, Szeto J-Y1, Isaacs MD1, Gealy EC1, Rose R1, Scoeld S1,
Watson PD1, Hayes AJ1*
1Bioimaging Research Hub, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX.
Wales, UK
EMS Engineering Science Journal
Research Article
Cite this article: Hayes AJ. Production of 3D Printed Scale Models from Microscope Volume Datasets for use in STEM Education.
EMS Eng Sci j 2017, 1(1):002.
*Corresponding author : Dr. Anthony J.
Hayes, Bioimaging Research Hub, Cardiff
School of Biosciences, Cardiff University,
Cardiff CF10 3AX, Wales, UK,
Tel: +44(0)2920876611;
Email: hayesaj@cardiff.ac.uk
Received: 19-06-2017
Accepted: 20-06-2017
Published: 21-07-2017
Copyright: © 2017 Hayes AJ
Abstract
Understanding the three-dimensional morphology of a biological sample at the mi-
croscopic level is a prerequisite to a functional understanding of cell biology, tissue
development and growth. Images of microscopic samples obtained by compound
light microscopy are customarily recorded and represented in two dimensions from
 -
mation. The commercialisation of fast, laser-based microscope systems (e.g. confo-
cal, multi-photon or lightsheet microscopy) capable of generating volume datasets of
microscopic samples through optical sectioning, coupled with advances in computer
technology allowing accurate volume rendering of these datasets, have facilitated sig-
    
       
generating morphologically accurate, physical models from these microscope volume
           
replicas will provide improved sensory perception, offering tactile as well as visual
interaction, leading to improved understanding of structure function relationships.

Z-stacks of optical sections from confocal and lightsheet microscopes using afford-
-
ed models of a variety of different biological samples at a range of scales including
pollen grains from two species of plant; blood cells from both human and earthworm
species, a section of plant root; the compound eye of an ant; and a developing Ze-



Keywords: Confocal Microscopy; Lightsheet Microscopy;
    -
ing
Introduction
 -
cantly as a transformative technology in recent years with
dramatic improvements in printing speed, resolution and

      

resin, plastic, metal), each with their own advantages and
       
-
  -

resonance (MR) scans and to generate implants and prosthet-
-



and teaching applications. The potential of the technology to

also slowly becoming realised, with a handful of recent stud-
ies describing approaches for the creation of physical mod-


Cite this article: Hayes AJ. Production of 3D Printed Scale Models from Microscope Volume Datasets for use in STEM Education.
EMS Eng Sci j 2017, 1(1):002.
els from volume datasets obtained by both light microscopy
       
 
-
        -
 


basis – the resolution of the print being determined by the
thickness of the printed layer.
  

volume datasets obtained by confocal and lightsheet mi-
    
-
       
samples from both plant and animal species and range in scale
from the level of cell organelle to multicellular developmen-
 
 
compatible with all imaging modalities that generate volume
-
croscopy, spinning disc microscopy, multi-photon microsco-
py etc) and thus can be applied to a variety of microscopy
platforms and image processing and analysis software. The
       
-
nology, engineering and math) activities, science education,
and outreach and engagement programmes.
Materials and Methods


Samples
To evaluate the methodology, a range of different biological
samples from single cells to multicellular organisms, includ-
ing both plant and animal species, were imaged using con-
focal or lightsheet microscopy. Images were generated from


Commercial unstained slide preparations of (a) pollen grains

latifolia); (b) erythrocytes from a human blood cell smear; (c)
a transverse section of root from the Lilly of the valley plant
-
kocytes (coelomocytes) obtained from the coelomic cavity of
 -
-



and cell nuclei (further details below). All image acquisition
-

Image Acquisition
Confocal Microscopy
  -
sheet microscopy (see below), all other samples were imaged
      
   
-
pour deposition with gold using standard scanning electron
microscopic procedures. Confocal microscopy of the samples




Cite this article: Hayes AJ. Production of 3D Printed Scale Models from Microscope Volume Datasets for use in STEM Education.
EMS Eng Sci j 2017, 1(1):002.
   
system (Zeiss, Jena, Germany). Individual samples were vi-
  
 -
-
rived from each sample using spectral (lambda, wavelength)
   -
-
sions collected sequentially across the visible range and into


thus inform appropriate scan parameters (refer to table 1).


applying Nyquist sampling criteria and a pinhole size of 1
Airy unit (AU) to give the best signal to noise ratio. Line av-
eraging was used for electronic noise reduction throughout.

confocal software) or .czi (Carl Zeiss Image) formats.
Lightsheet Microscopy
Lightsheet microscopy, performed using a Zeiss Lightsheet
Z.1 system (Zeiss, Jena, Germany), was utilised for whole or-
    
     
-


      

agarose, drawn into a warmed capillary tube and then loaded

-
trast)
  Laser line
(nm)

bandwidth
(nm)

-
cence)



oil
 
Bulrush pollen
-
cence)
 
oil
 

-
cence)
 
oil
 
Compound
-


  -
rescence)
-
tance)

-
cence)

-
tance)
Root section
-
cence)
 
oil
 

-

nuclei)
Lightsheet
Z.1
  







   

 
to optimise the signal from these emission peaks.
into the specimen chamber of a Zeiss Lightsheet Z.1 micro-

       -
 -
tation and emission settings for simultaneous recording of
  
   

      


Cite this article: Hayes AJ. Production of 3D Printed Scale Models from Microscope Volume Datasets for use in STEM Education.
EMS Eng Sci j 2017, 1(1):002.
Volume Reconstruction and Surface Rendering

    -
ford Instruments). Z-stacks of optical sections from each
       
       


rendered via absolute intensity thresholding with smoothing
        -
         -
Lab (), which is a free, open source
software platform that provides additional editing tools to
-
   -


also provides an advanced toolset that will allow generation
-
croscopy platforms.
3D Printing and Processing
   -
         
        -
   
        
      
-
       
       


then printed overnight. Once each print was complete, the
         
supporting scaffold carefully detached from the model using
   
models that were outside the print bed parameters (e.g. the

printed as separate halves. The complementary halves were

  
(e.g. smoothing of edges from support stubble) was per-
formed using a paint brush dipped in acetone. A water-based
acrylic paint was used to contrast features of interest in the

Results
Plant Pollen
   -
mon daisy (Bellis perennis) and Bulrush (Typha latifolia)

  -

focal Z-stacks through individual grains provided striking

     
provided volume overviews of the pollen grains and demon-
      
   
grains were spheroidal in morphology with prominent spiny
-
as Typha grains were grouped into tetrads, with reticulate
       
showed further topographic detail of the surface ornamenta-
-


-


     


Human Erythrocyte
Confocal visualisation of human blood smears revealed a
     
the green and red range of the visible spectrum. As the cells
were closely associated, we employed a circular ROI (region
of interest) to delineate a scan area around individual eryth-
rocytes. Confocal Z-stacks through the cells showed a disc
       
thickness at the centre of <1 micrometre, in agreement with
-
constructions showed the characteristic biconcave morphol-
  
process a clipping plane was introduced through the erythro-
cyte disc diameter so that the model could be printed in two
halves in order to convey the biconcave discal morphology

Earthworm Leukocyte (chloragocyte)
Chloragocytes obtained from the coelomic cavity of the earth-

       
     
-
-
-
nal from the chloragosomes, which were modelled in green,
 
        
        

surfaces and reveal topographic detail of the chloragosomes

Plant Root

Cite this article: Hayes AJ. Production of 3D Printed Scale Models from Microscope Volume Datasets for use in STEM Education.
EMS Eng Sci j 2017, 1(1):002.


  -




I. Cut plane model showing internal surface structure of intine (dashed line indicates clipping plane).


supports are detached after printing.


Cite this article: Hayes AJ. Production of 3D Printed Scale Models from Microscope Volume Datasets for use in STEM Education.
EMS Eng Sci j 2017, 1(1):002.
      -
    (Con-
vallaria majalis)
  

used to generate Z-stacks of optical sections through the tis-
  -
    -


internal architecture was faithfully replicated at high resolu-

Insect Compound Eye
     
through the compound eye of an ant (Myrmica rubra) re-

    -
  
   -
ple with gold provided a similar level of surface detail of the
       
-

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
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        
       
      

comprising head, trunk and tail, arched around the yolk sac.
-
ial structures of the spine including neural tube, notochord,
the somites and their boundaries. The topography of these
internal structures was manifest in the surface-rendered


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
      
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

Cite this article: Hayes AJ. Production of 3D Printed Scale Models from Microscope Volume Datasets for use in STEM Education.
EMS Eng Sci j 2017, 1(1):002.
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B. The erythrocyte model was printed in two halves to convey the characteristic biconcave morphology visible in histological section planes. The support raft
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
associated root cells are visible.



-



Cite this article: Hayes AJ. Production of 3D Printed Scale Models from Microscope Volume Datasets for use in STEM Education.
EMS Eng Sci j 2017, 1(1):002.
 
-




Cite this article: Hayes AJ. Production of 3D Printed Scale Models from Microscope Volume Datasets for use in STEM Education.
EMS Eng Sci j 2017, 1(1):002.
Discussion
This paper describes methodology for the generation of scale
       -
scope volume datasets for use in science engagement and
      
-
         
technique can be utilised with any imaging platform that gen-
erates volume datasets through optical sectioning. Using the
-

   -
rescent proteins, or by sputter coating of samples by physical


-
   
mesh. This approach would therefore be useful for intracel-
      
   -
mentation post-acquisition, either through grey value thresh-

In this study we have utilised high-end image analysis soft-
     
      
 
  -
   -
   
    
this study is therefore minimal, with a typical cost of around
 
with printing times of around 8 hours. The methodology
   


can be used as masters to generate moulds that would allow
rapid bulk casting of the models or permit the use of novel
fabrication materials.
        
        -
      -
dered in silico
presenting haptic as well as visual cues about structure and
        
      

well as providing complementary tactile information about
microscopic specimens, we have also found the models to be
     -
     


visually impaired individuals or those with other physical or
    
 
-
tance to society, as it encompasses and integrates a variety of
-
ence, technology, engineering and maths. It is therefore used
in our undergraduate teaching and training programmes and
for science outreach and engagement activities.
   
information about microscopic structure and function in sci-
ence education and research is slowly becoming realised. A
small number of recent studies have implemented additive
manufacturing techniques to generate physical models from
 -
       
skeletal muscle cells from confocal datasets; whereas both


is broadly similar to these studies, by applying a variety of
sample contrast techniques, different optical imaging modal-

-
ology.
Additive manufacturing is still an evolving technology and
whilst its advantages are considerable, it has some notable
disadvantages which include print reliability, resolution,
           
        
    

      
of the print raft to the heated print bed, and other technical
issues associated with this format. In this study we applied
     
an acceptable compromise between resolution and speed

this kept layering artefacts to an acceptable level, there was

the original microscope dataset. However, it is worthwhile
noting that greyscale thresholding, required to generate the

  
following removal of the print scaffold, which leaves minor
         
-
    -
  


then subsequently fused together.

delivering measurable improvements in additive manufac-

        


Cite this article: Hayes AJ. Production of 3D Printed Scale Models from Microscope Volume Datasets for use in STEM Education.
EMS Eng Sci j 2017, 1(1):002.
two colours or with different printing materials (e.g. resin,

      
  
-
ther reducing costs. The cost of the printers themselves and
their printing materials has also tumbled, now making them
viable standard laboratory acquisitions. It is anticipated

printing as a transformative technology and, in the current

the microscopic world.
Author Contribution:

Acknowledgements


   

   -
 -
scan confocal microscope, Zeiss Lightsheet Z.1 microscope
       

Infrastructure fund.
References
1.        
     

        
    

 -
        

    
  -
    

5.     
production of anatomical teaching resources using three-di-
       

6.         


   -
        -
      
.
8. 
 


 Bagley JR, Galpin AJ. Three-dimensional printing of hu-
 
 


-

11. 



a new take on an old method for generating high-resolution
   







        

16.          

  

    -
-

18.         



 -
      
      -


Cite this article: Hayes AJ. Production of 3D Printed Scale Models from Microscope Volume Datasets for use in STEM Education.
EMS Eng Sci j 2017, 1(1):002.
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        

-

-


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       
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