ss lab project write up
TRANSCRIPT
SS Geology Lab Project
3d Modelling Technique Development Using Estonian Bio-Eroded
Ordovician Bryozoa
Michael O’Hanrahan – 12306206
February 2016
TABLE OF CONTENTS
1. Abstract .................................................................................................................1
2. Introduction .........................................................................................................2
3. Methodology ........................................................................................................3
3.1. Sample Preparation ........................................................................................3
3.2. Imaging ..............................................................................................................4
3.3. Stacking and Alignment..................................................................................5
3.4. Importing To OsiriX ........................................................................................7
3.5. Model Rendering..............................................................................................8
3.6. Exporting Models .............................................................................................9
4. Results ................................................................................................................ 11
5. Discussion.......................................................................................................... 13
6. References ......................................................................................................... 14
1
1. ABSTRACT
The concept of this Senior Sophister lab project was to sequentially slice ordovician Bryozoa in an
attempt to create a three dimensional model highlighting interior bio erosion within the specimens. It
was aimed to create a model of sufficient detail that the interior features could be quantitatively
analysed to create a diagnostic report on the morphologies of these organic, parasitic marks and
possibly identify the species that created these features. The project was approached using modest
equipment and mostly free, open source software to ensure easy replication of methodologies. The
methodologies detailed herein achieved volumetrically accurate three dimensional models using the
medical software OsiriX. Some issues arose due to low sampling rate and a revised methodology is
detailed in the discussion in an attempt to maximise efficiency and resolution of results.
2
2. INTRO DUCTIO N
This Senior Sophister lab project was undertaken in October 2015 with the aim of developing three-
dimensional digital models of bioerosion within Ordovician bryozoa samples collected in Estonia.
These models were intended to be used in the quantitative analysis of the bioerosion and possible
diagnosis of the boring species based the volumetric analysis on the apparent morphology of the
borings.
Using only equipment available at the time of this project in the Museum Building geology
laboratory of Trinity College it was decided that the best method to approach this modelling was to
employ a technique based on slice based tomography. Several challenges and questions were apparent
from the idea’s conception. It was not known whether the spatial resolution would be adequate between
slices to create a seamless model. The saw used was also an anticipated issue, using the saw available it
was speculated that the width of the cutting edge would cause a detrimental loss of spatial information.
Another notable challenge was that there were few documented cases available of three dimensional
palaeontological models being produced with non-specialised equipment or free software so the
techniques employed herein are the result of many trial and error approaches.
3
3. METHO DO LO GY
3.1. SAMPLE PREPARATIO N
Samples for modelling were chosen upon the potential prominence of the bioerosion within. The more
bioerosion present in the sample, the easier it would have been to visually detect in the sample and
software detection stages. Two different sets of sample preparation were available, one was devised for
this project and another from a previous, unsuccessful attempt at bioeroson analysis.
The latter group of samples were available as slices of ordovician bryozoa. Several layers of
lacquer were applied to these samples, named ‘Estonia specimen 2’, ‘Estonia specimen 3’ and ‘Estonia
specimen 4’ respectively, in an attempt to increase the contrast between the bryozoan and the internal
sediment that infilled the bioeroded cavity. These samples were scanned on both sides in a flat bed
scanner on the highest resolution setting available (1200dpi) with a 10mm scale bar for later software
calibration. The samples were cut with no guide in a rock saw with a 2mm cutting edge diameter. The
resulting slices varied in thickness were averaged to 4mm with an accurate calliper. It is worth noting
that not all slices were parallel so some inaccuracies were expected in later stages.
Fig 3.1.1 Lacquered and scanned samples of the Estonia specimens 2,3 and 4 with a 10mm scale bar.
Lighter coloured, elongate shapes within the samples are the areas of interest created by a variety of
organisms boring the bryozoa as it grew concentrically outward from the center of the flat base.
The problems recognised above in the available Estonia specimen slices were expected to
cause an issue with the accuracy in later modelling. To overcome the issues of parallel slicing and in an
attempt at making slices more consistently spaced it was necessary to devise a guiding mechanism for
the sawing stage of preparation. With this in mind it was decided to mount the somewhat round sample
(named ‘Ristna Cliff specimen’) in a semi transluscent resin block with straight edges to allow the
4
block to be fed into the saw blade and ensure slices were consistently orthogonal to the straight edge. It
is worth noting that the resin mouting also benefits the later digital alignment stage. Feeding the sample
into the saw was done by hand to the smallest increment possible while still retaining a rigid slice, this
thickness proved to average at approximately 3mm which is an important parameter to later digital
reconstruction. It was then necessary to label all the slices clearly and methodically with an indelible
marker making sure to denote the number of the slice and also the face. In this example each face was
denoted as either ‘a’ or ‘b’ to ensure the slices could be assembled in their original orientation relative
to each other.
Fig 3.1.2 Illustrates the pre-slicing preparation for the ‘Ristna Cliff specimen’ Image 1 shows the foil
casing into which the resin was poured and hardened, Image 2 illustrates the resin block with the edges
shaved off in preparation for slicing, Image 3 shows the first slice (1a) from the block (not lacquered)
with a scale bar for later software calibration.
3.2. IMAGING
Imaging in this project was approached in two different ways , both of which posed no apparent issues.
The first approach was to use a flatbed scanner with a high resolution setting. The second imaging
technique incorporated the use of a Canon Eos 70d DSLR 20.2 effective megapixel sensor camera
coupled with a Canon EF 100mm f/2.8 Macro USM lens. Both techniques yielded results with
negligible differences in image quality and resolution.
The Estonia specimens 2-4 were all scanned in the flatbed scanner as well as a later lacquered
sample of the Ristna Cliff specimen. All slices were scanned on both sides with a scale bar, as seen in
Fig 3.1.1, and exported to a 1200dpi .tiff file to ensure that maximum resolution would be achieved.
To photograph the Ristna Cliff specimen after the resinous mounting block had been sliced ,
the 70d DSLR was set up on a table with two fluorescent bulbs to the left and right of the sample space
and a white sheet of paper as a background. A corner mark was drawn on the paper to aid alignment
between sequential photographs and a scale bar was included in the first image as seen in ‘image 3’ of
Fig3.1.2. Photographed in sequence, the images were captured at an aperture value of f/10 to en sure
maximum depth of field and sharpness in focus. The images captured were recorded as uncompressed
camera raw image file (.cr2) to ensure the maximum amount of information was captured in the
interest of later sharpening. The camera raw files were imported to a raw processing software (in this
5
case ‘Adobe Lightroom 6’) for white balancing, contrast adjustment and sharpening before exporting
as high resolution .jpeg files which were individually named with their respective slice numbers.
3.3. STACKING AND ALIGNMENT
All recorded images were stacked and aligned in Adobe Photoshop CS6 and exported as high
resolution .jpeg files. The scanned images necessitated a slightly different workflow to achieve a
coherent, aligned stack of 2d images. The workflow that follows is what proved to be the most
effective for the imaging approaches detailed above and is specific to the Adobe Photoshop CS6
program but similar results can be achieved in other (free) imaging softwares that allow for images to
be layered and those layers to be exported as individual .jpeg images such as GIMP (‘GNU image
manipulation program’).
In order to obtain the required aligned stack of images from the scanned files it is first
necessary to open the scanned .tif in Photoshop. The image will appear as the Estonia specimens are
shown in Fig 3.1.1 as one layer in the right hand panel. Using the ‘magic wand’ selection tool the first
slice must be selected and cut or copied to a new layer. The the automatic selection will be sufficiently
accurate but it is suggested that the edges are refined to ensure that the resulting layer contains as much
edge detail as possible. Using the ‘refine edge’ tool a more accurate selection can be achieved with
parameters suggested below in Fig 3.3.1. It is imperative to include the original scale bar from the scan
in the stack of layers.
Fig 3.3.1 This figure shows a selection of the area of interest that will output to a mask, making any
areas not in the selection transparent. The radius, smoothing, feather and cont rast values are chosen for
the best possible selection.
Once the selection is output to a new layer with a layer mask it is recommended that it is
named according to the relevant slice number. This will ensure that with later exporting the layers will
be appropriately labeled and in sequence. This process needs to be repeated for all layers such that a
6
stack of layers is generated with only the relevant areas are visible. Upon completing this step it is then
necessary to align the images to their original orientation.
To align the scanned images it is best to drag all layers in their correct order to a central point
using the ‘move’ tool. To ensure that the inner features, in this case the bioerosion caused by
polychaete worms and boring bivalva, line up appropriately. It is necessary to flip one of the groups of
faces (i.e. all ‘a’ or ‘b’ faces) horizontally (use Edit Transform Flip horizontal). After this step is
completed it is necessary to align all of the 2D slices into their original orientation. Using the move
tool and directional keys the layers must be moved to align with eachother, it is recommend ed that the
alignment should begin with the first slice and worked through to the end linking the corresponding ‘a’
and ‘b’ faces together. The final stack will be similar to that shown in Fig 3.3.2, below.
Fig 3.3.2 Is an 2D end view profile of Estonia specimen 2 layered and aligned in Photoshop.
The photographed specimens follow a similar procedure once imported. Layers must be
generated in the manner detailed above, however, with the Ristna Cliff samples the resinous mount
makes the alignment stage much more accurate. Using the edges of the resin block, the layers can be
aligned as they were originally i.e. before slicing, this greatly reduces the margin for human error in
this stage of the process (see: Fig 3.3.3 overleaf)
7
Fig 3.3.3 This figure represents a stacked and aligned 2D end view profile of the Ristna Cliff specimen
with a 10mm scale bar.
3.4. IMPO RTING TO OSIRIX
Using a slice based approach to 3D rendering these specimens was deemed the most appropriate
solution to be able to capture the internal bioerosion of interest. Medical professionals have used
similar slice-based approaches for magnetic resonance imaging (MRI) and computed tomographic
(CT) studies from which there are often 3D quantitative models made for diagnostic purposes. A
common program for such rendering is OsiriX which allows the user to visualise multidimensional
images and build them from 2D images. OsiriX offers a free version of software for demontration
purposes which limits the maximum mount of images that can be loaded into one model The OsiriX
software is designed to work with DICOM (.dcm) file formats which are produced by medical imaging
equipment to contain all image files as well as spatial imaging information and patient details.
The Estonian specimen images recorded would have to be converted from .jpg file format to
.dcm file format to overcome a compatability issue. In this situation it was found that a plug-in on the
OsiriX ‘plugins manager’ named ‘JPEG to DICOM’ was necessary for this conversion. Using the plug -
in simply required creating patient information to be able to import stacked .jpg images of specimens.
The specimen appeared as a patient file and the 2D viewer tool allows the user to view a dynamic
video scrolling through the layers of a file which is reminiscent of the videos output by MRI imaging
equipment. A DVD-R is attached with this project containing sample image files and rendered video s
of panning models , a sample 2D video of Estonia Specimen 2 is attached with the file name ‘Estonia
Specimen 2 2D scroll’ within the folder ‘Estonia Specimen 2 2D Scroll.mov’.
8
3.5. MO DEL RENDERING
Once imported into OsiriX and loaded in the ‘2D Viewer’ panel was then possible to begin rendering
the three dimensional models. Calibration of the dataset proved to the most critical step to rendering,
which makes the inclusion of a scale bar from the outset imperative to having a spatially accurate
model. Two types of rendering are possible with these datasets, 3D volume rendering and 3D MIP
(maximum intensity projection).
To first calibrate the software it was necessary to find a frame of the ‘2d scroll through’ in the
‘2D Viewer’ panel. Once the frame was found a straight line ROI (region of interest tool) was used to
measure the length of the line, initially it was represented in pixel values as the .jpg files do not, by
their nature, contain spatial information other than pixels. By clicking ROI ROI info…
Recalibrate and inputting the length of the measured scale bar it is possible for the software to now
actively convert the pixel values to centimeters. With the dataset then calibrated to centimeters the
spatial information of the 3D slice thickness correlates to the width of the 2D scale bar in the .jpg
image.
3D volume rendering using these datasets proves to be useful for the visualisation of external
shape of the model. Using a certain values of pixel X and Y resolution (0.3 in these sets) coupled with
a slice interval (determined from averaging the thickness of each physical slice of the sample after the
slicing stage of sample preparation) a model can be rendered in full colour.
Fig 3.5.1 This figure shows a 3D volume rendering of Estonia Specimen 2 in full colour, left is a
corner view, middle is an end view profile, right is 90° horizontal to left. A video rendering of this
panning is supplied on accompanying disk, the file is named ‘Estonia Specimen 2 Volume Rendered’.
3D MIP allows the user to highlight areas of interest through a multitude of colour look-up
tables. The technique creates a colour profile based on colour wavelength which can be varied by the
user in order to make certain colour wavelengths stand out while others become transluscent. The
standard colouring of the fossil as it exists naturally rendered a model that can be seen in Fig 3.5.2.
9
Fig 3.5.2 This figure shows three separate orientations of a 3D MIP rendering of Estonia Specimen 2,
left and right are 180° to each other. Interior bio erosion is not apparent. A 360° pan of the model is
attached in the accompanying DVD in a file named ‘Estonia Specimen 2 3D MIP 360° Pan.mov’
In an attempt at isolating the bio erosion within the sample using 3D MIP a colour lookup
table (CLUT) is applied to the rendered model. The most effective CLUT for this example proved to be
‘NIH’ where the bio eroded areas appear a ‘hot white’ colour within the model.
Fig 3.5.3 This figure illustrates the isolation of areas of interest within the internal strucure of the
specimen using the ‘NIH’ CLUT in 3D MIP rendering. In the attached DVD there are three related
.mov files: ‘Estonia Specimen 2 CLUT 2D Scroll Through .mov’, ‘Estonia Specimen 2 CLUT 3D MIP
Vertical Pan’ and ‘Estonia Specimen 2 CLUT Horizontal Pan’.
3.6. EXPO RTING MO DELS
10
The models created were exported as .mov files for illustrative purposes. Once the stacks of images
were rendered as 3D volume renders or 3D MIP it was possible to export the models at a chosen
rotation speed and angle by clicking file export export to movie… Similarly it was possible to
export high resolution TIFF, JPEG and RAW images.
11
4. RESULTS
Several models were successfully produced from the sequential slice based imaging approach that is
detailed above. The results show that volumetrically accurate 3D models can be made with relativ ely
modest equipment provided that measurements are taken and translated into the dataset calibration
stage of the rendering process.
3D volume rendering was effective in producing a digital representation of the exterior of the
specimens chosen but the shape is directly effected by the number and spacing of the samples. It is
quite apparent in Fig 3.5.1 that the exterior surface in the final model is not as well rounded, smooth
and continuous as the original, physical specimen. It is also quite clear that while the end of each
specimen was scanned and/ or photographed the profile of this slice has rendered as a flat shape in it’s
three dimensional representation.
Fig 4.1 This figure shows the use of an ROI tool as a straight line measuring tool in OsiriX where the
diameter of the slice 1a of Estonia Specimen 2 is 3.45cm which is consistent with the original, physical
specimen.
12
3D MIP rendering appears to hold similar issues with exterior representation being relatively
rough in shape and flat on each end. The interior bio erosion, while successfully highlighted on the
external face of each layer, dos not appear as continuous from one slice to another. Instead of
appearing continuous the prominent internal features of the specimens, displayed for example in Fig
3.1.1, remain only on the plane of slicing and are not interpolated from point -of-entry to point-of-exit.
While the models were successfully rendered from 2D into 3D using Photoshop and OsiriX
the original aim to digitally diagnose the morphology of the bio erosion is still not possible. Further
attempts to do so with these samples will realistically yield the same results with no viable way of
reliably measuring the interior features. More accurate sample preparation would be reccomended with
a higher sampling rate (i.e. more accurate slicing, with closer spacing and more precise machinery).
13
5. DISCUSSION
While the results show that three dimensional models of volumetric, quantitative merit are possible to
create using modest equipment, there are some significant disadvantages.
The most obvious disadvantage with the above approach is that the volume rendered in the
models is not extremely detailed. The edge detail of each slice, while sharp in 2D, renders as soft and
stretched in 3D. This is likely a result of the relatively low sampling rate over the diameter of the
specimen. If possible, it is recommeded that in order to create a highly detailed rendering of the
external surface of a specimen that the sample rate (or slice interval) be much higher. In the case of
these samples the average slice interval proves to be around 3mm, the smaller the interval the more
smooth the transition between slices would be and the higher the spatial resolution would become. A
practical solution to this issue would be to use a serial grinding technique where, instead of slicing, the
sample is effectively shaved down slightly on one edge and polished by different abrasive plates. While
this suggested method might be destructive of the sample the slice interval could be reduced to a
micron scale. This method is well detailed in a study by (Pascaul-Cebrian et al. 2012) where the
sequential grinding of a block incorporates an automatic scanning mechanism once a layer several
microns thick is removed allowing for an extremely continuous sampling rate and results in an
extremely smooth 3D volume rendering. The saw used to slice the specimens in this project was a very
coarse approach in comparison and the width of the saw blade (2mm diameter) would have caused
2mm of information loss between each slice.
The approach of selecting and layer masking each slice in Photoshop is extremely time
consuming. Selecting each image and customising each mask for the ideal edge selection proved to be
very laborious and has potential for further automation. Photographing the specimens was presumed to
allow better resolution images to use for modelling but it does not appear to provide any significant
advantages and the associated extra steps in editing add to the hands-on, laborious nature of the
imaging aspect of the sample preparation stage. Scanning of the images provides adequate image
resolution and saves considerable time on digital image preparation.
To revise all techniques used above and to acknowledge the ideal workflow to achieve the
best results while maximising efficiency may be of value to conclude with. Ideally the sample would
be mounted in a guiding block similar to that of the Ristna Cliff sample, this proved to aid in the
accuracy of slice angles and alignment. The saw used would need a far smaller diameter blade to
minimise the amount of information lost with each cut. A guiding mechanism that would feed the
sample in to the saw blade at a definite interval would be highly recommended and would ideally be
able to achieve an advancement of the sample into the saw on the scale of at least one millimeter
depending on the scale of the sample and size of areas of interest. The imaging is is quickly and
efficiently achieved with a flatbed scanner so there is little need for DSLR type camera imaging. With
a well made mounting block and a continuous edge across all slices, alignment could be automated in
Photoshop using the ‘auto-align’ tool, further reducing time expended in preparation. There is no
obvious way, however, to reduce time spent creating layer masks to digitally extract the specimens
from their mounting, which is certainly an area for further experimentation.
14
6. REFERENCES
1. Pascual-Cebrian, E., Hennhöfer, D.K. & Götz, S., 2012 3D morphometry of polyconitid rudist
bivalves based on grinding tomography Facies April 2013, Volume 59, Issue 2, pp 347-358