OPTARC PUMA User manual

PUMA Foundation Scope
User’s Manual
Document created: 03.07.2021, Last edited: 12.08.2021
Manual prepared by OptArc − Designers and
manufacturers of custom optical and
optoelectronic systems using 3D printing
rapid prototyping and based in the UK.
See optarc.co.uk for details.

Safety Information
Identification of risk
Throughout this manual please take heed of arnings given in bold text and
highlighted yello to a oid possible damage to equipment and/or harm to people.
Risk to vulnerable groups
PUMA microscopes and associated systems are not toys. They contain small parts which
may come loose such as tiny metal screws and washers and glass components that may
splinter or break or otherwise present a choking or sharp object hazard or chemical
hazard (e.g. for batteries). Please do not let babies or young children play ith or gain
access to any aspect of a PUMA system ithout close appropriate adult supervision.
Like ise keep PUMA systems a ay from pets.
Risk of damage to eyesight
When choosing and using a light source for a PUMA microscope, care must be taken to
a oid the use of or exposure to light that could damage eyesight.
In particular never allo direct or specular reflections of the sun to enter the
microscope through the illuminating mirror.
Also, never allo laser light to enter the microscope through the illuminating mirror
if any vie ing is to be done by eye (as opposed to recordings by a camera only).
ownload link for P F version of this Manual
PUMA Foundation Scope Page 2 of 40 User’s Manual v1.0
You can download the latest ersion of this User’s Manual
as a PDF file from the Support section of the OptArc
website ia this link:
https://www.optarc.co.uk/support/

Contents
Safety Information.................................................................................................................... 2
Identification of risk............................................................................................................. 2
Risk to ulnerable groups.................................................................................................... 2
Risk of damage to eyesight................................................................................................. 2
Download link for PDF ersion of this Manual.......................................................................2
Legal Information..................................................................................................................... 5
Copyright.............................................................................................................................. 5
Trade Marks.......................................................................................................................... 5
Limitations of Use................................................................................................................ 5
Disclaimer............................................................................................................................. 5
Discrepancy in Appearance of Parts...................................................................................5
Abbre iations............................................................................................................................ 6
Introduction.............................................................................................................................. 7
PUMA.................................................................................................................................... 7
Foundation scope................................................................................................................. 7
Anatomy of a PUMA Foundation Scope........................................................................8
Unboxing and Initial Assembly.............................................................................................. 10
Unboxing............................................................................................................................. 10
Assembling the Microscope.............................................................................................. 13
Filter slider trays and retention collars............................................................................18
Making Obser ations............................................................................................................. 19
How to place a specimen on the stage.............................................................................19
How to focus the scope..................................................................................................... 20
Attaching a camera............................................................................................................ 20
Eyepiece Camera........................................................................................................... 21
C-Mount Camera........................................................................................................... 21
Smartphone Camera..................................................................................................... 21
Ad ice for Good Illumination................................................................................................. 22
Upgrades................................................................................................................................. 24
Higher Magnification......................................................................................................... 24
Long Legs System.............................................................................................................. 25
Abbe Condenser................................................................................................................ 26
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Köhler Illuminator.............................................................................................................. 27
Trans-Polarising Module................................................................................................... 28
Ad anced Filter block........................................................................................................ 28
Epi-illumination................................................................................................................. 28
XY Mechanical Vernier Slide Holder.................................................................................29
Trinocular Port................................................................................................................... 29
Augmented Reality (AR) Projector for Heads-up display (HUD)....................................29
Spatial Light Modulator (SLM)..........................................................................................29
Binocular Head................................................................................................................... 29
Z-Motor.............................................................................................................................. 30
Maintenance............................................................................................................................ 31
A oid excessi e heat.......................................................................................................... 31
Moisture and condensation............................................................................................... 31
Lens care............................................................................................................................. 31
Lubricating the focus mechanism....................................................................................32
Adjusting the belt tension................................................................................................. 34
Adjusting the optical axis of the optical tube..................................................................35
Disposal and Recycling.......................................................................................................... 37
Recycling of PLA Plastic in the UK....................................................................................37
Recycling of PLA Plastic outside the UK...........................................................................37
Electronics.......................................................................................................................... 37
Index........................................................................................................................................ 38
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Legal Information
Copyright
This user’s manual is copyright © 2021 by Dr Paul J. Tadrous. All rights reser ed.
Trade Marks
OptArc and the OptArc logo are Registered Trade Marks of Dr Paul J. Tadrous
(registered with the UK Intellectual Property Office).
Limitations of Use
The PUMA microscope and its associated systems do not ha e any certifications or
regulatory appro als in any country for use in clinical diagnostics or treatment (human
or eterinary).
The PUMA microscope and its associated systems are released to be used for research
and educational purposes only.
isclaimer
All PUMA project information, including without limitation any CAD file or STL file and
all documentation, ad ice and instruction (whether pro ided in ideo form, audible
form, written form or otherwise) is pro ided ‘as is’ in good faith and is intended to be
helpful but comes with no warranty whatsoe er.
Anyone attempting to build or use a PUMA microscope or other PUMA-related material,
accessory, module or deri ati e is hereby ad ised that there will be risk in ol ed in 3D
printing, post-print processing, assembly and usage of the resulting structures. This risk
includes, without limitation, the risk of personal damage and loss of resources.
Dr Paul J. Tadrous, TadPath and OptArc cannot accept any liability for any such loss or
damages that may occur. All those who attempt to build or use any aspect of the PUMA
project or deri ati es thereof do so at their own risk.
iscrepancy in Appearance of Parts
The parts in your package may differ in exact appearance to the parts shown in this
manual or in the associated ideos or ad ertising materials because we always ship the
latest ersions of the scope and the manual and ideos may ha e been prepared using
earlier models. Functionality of the parts you recei e will be the same or better than
those illustrated in this manual and any associated ideo or ad ertising materials.
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Abbreviations
Some common abbre iations used in this manual are listed below for con enience.
AR Augmented Reality
CAD Computer Aided Design
HUD Heads-up Display
IC Integrated Circuit
LED Light Emitting Diode
NA Numerical Aperture
PLA Poly-lactic acid
PUMA Portable Upgradeable Modular Affordable
QR Quick Release (mechanism for attaching the optical tube)
RMS Royal Microscopical Society
SLM Spatial Light Modulator
STL Stereolithography file (a file format for meshes)
PUMA Foundation Scope Page of 40 User’s Manual v1.0

Introduction
PUMA
PUMA is an open source 3D printed high quality customisable
microscope system. The name PUMA stands for P ortable,
U pgradeable, M odular and A ffordable – key features of this
system. To learn more about the
PUMA open source project and
to get CAD files, software and
schematics please see the
official PUMA GitHub repository:
Foundation scope
The Foundation scope is the simplest configuration of a PUMA
system that can be used as a working microscope. This
configuration is made a ailable for sale by OptArc so that people
who, for whate er reason, don’t want to build a PUMA scope from
scratch using DIY 3D printing can easily get started with PUMA.
Anyone with 3D printing and DIY abilities could also make their
own Foundation scope using the standard PUMA modules and
specifications a ailable on the GitHub page.
It is called ‘foundation’ because you can use this scope as a starting
point from which to swap in arious optional extra modules to
build any of the other PUMA configurations all the way to an
ad anced research microscope with motorised Z-stage and TFT
screens for augmented reality optical image o erlay and Fourier
optics digital light processing, binocular or trinocular iewports,
fluorescence, phase contrast, polarisation, and more.
Out of the box, the OptArc PUMA Foundation scope comes with a
high quality Plan Achromat x4 objecti e and a x10 high quality ocular
with good eye relief and a wide exit pupil for comfortable iewing.
Without further optional upgrades this scope will gi e a relati ely
low total magnification of x40 with a wide flat field of iew. With its
mirror illuminator alone this can be increased to x100 total
magnification using an optional x10 objecti e (sold separately).
If you want to use e en higher magnifications then you are ad ised to
add the PUMA Abbe condenser (this is an optional upgrade). See the
‘Upgrades’ chapter later in this manual for more complete
information about the arious upgrades a ailable.
PUMA Foundation Scope Page 7 of 40 User’s Manual v1.0
PUMA on GitHub
Foundation scope
OptArc high quality
x10 eyepiece
PUMA GitHub Page
https://github.com/TadPath/PUMA

Anatomy of a PUMA Foundation Scope
The names of arious parts of your Foundation scope are explained here. More detailed
technical specs and nomenclature are a ailable on the PUMA GitHub pages but this
information should be all you need for e eryday use of your scope and common
maintenance as well as understanding the instructions in the rest of this manual.
Note that these illustrations may differ in aspects of detail from your Foundation scope
because they were prepared with slightly earlier prototypes (for example the leg
spacers contain an extra nut on them which is not part of the spec of a modern
Foundation scope) but none of these differences in alidate the nomenclature.
PUMA Foundation Scope Page 8 of 40 User’s Manual v1.0

The terms LEFT and RIGHT refer to the user’s left and right when obser ing the
microscope from behind (which is where the primary user is most commonly expected
to be situated when making obser ations). This explains why those terms appear to be
re ersed in the front-on iew shown in the figure below.
The terms ‘stage’ and ‘baseplate’ are interchangeable. Baseplate is used more
commonly when referring to the undersurface of the stage. The term ‘Z-stage’ refers to
the whole focussing mechanism i.e. the stage/baseplate and the focus platform as
joined by the three focus post bolts with a timing belt and pulley mechanism (this
arrangement is known as the ‘tripost architecture’ of the Z-stage).
The ‘optical tube’ refers to all abo e-stage optics plus the objecti e and this fits onto
the focus platform ia a tri-helical flexure thread called the ‘quick release mechanism’
or simply the ‘QR mechanism’. This is composed of a male part (attached to the bottom
of the filter block and which contains the thread for the objecti e) which mates with a
female part that is an integral component of the focus platform.
The mirror illumination system is composed of se eral parts as shown. The mirror itself
is the glass o al mirror. This is fixed to the o al plastic ‘mirror holder’ which, in turn,
articulates with the ‘mirror suspend plain’ component. The latter component is held
against the baseplate by the ‘mirror-to-baseplate attachment’ ia two M4 thumbscrews
(illustrated in the section ‘Assembling the Microscope’ below).
There are other features present which are not described here because they are only
rele ant to scopes that ha e upgrades fitted. These will be described in any manuals or
tutorials pertaining to the fitting and use of those upgrade modules.
PUMA Foundation Scope Page 9 of 40 User’s Manual v1.0

Unboxing and Initial Assembly
Unboxing
The following describes the recommended procedure for
remo ing the contents of the box that your Foundation Scope
shipped in. This procedure was designed to protect the
sensiti e optics. An unboxing YouTube ideo has been
prepared to illustrate the following steps and can be accessed
ia the link shown.
Step 1. Ensure the box is opened from the top. Take care not to
damage the contents when opening (do not stick a knife in to cut
open the box sealing tape).
Step 2. Remo e the instruction manual and top loose packing
filler material to re eal the bubble-wraped package which
contains all the parts.
Step 3. Gently lift out the bubble-wrapped package from the box and lay it on a flat solid
work surface. Remo e the box and loose packaging filler material from the work area.
The package is enclosed in two layers of bubble wrap. Cut the tape to release the first
layer of bubble wrap. The parts will be seen – through the second, inner layer of bubble
wrap − in a ‘boat’ made from paper.
PUMA Foundation Scope Page 10 of 40 User’s Manual v1.0
Paper boat
PUMA Unboxing Video
https://youtu.be/EfecD0UGLDQ

Step 4. The paper boat is the bottom aspect. Ensure you keep the contents with this
‘boat’ side down while you cut the tape that holds the inner layer of bubble-wrap and
remo e it. Keep everything on the ork surface. from no until step 6 – do not try to
hold it freely in the air or the objective lens may fall through the bottom and be
damaged. Remo e the small white box that contains the ocular lens and put it to one
side on the work surface. (as shown). Cut the tape that holds e erything in place in the
‘boat’ and remo e the simple filter block and the monocular tube and lay them to one
side. Also remo e the mirror packet and put it to one side.
Step 5. Remo e the test slide in its protecti e
case by sliding it out from under the timing belt
as shown.
PUMA Foundation Scope Page 11 of 40 User’s Manual v1.0
Remove the eyepiece box
Mirror packet

Step 6. Tear the paper at the back of the paper boat and open out the paper but do not
remo e it from under the package of parts yet – keep it in situ. Keep one hand over the
top aperture as sho n in the picture and slo ly rotate the stage up so you can access
the bottom aspect here the objective ill come out. It is only held there by a piece
of sticky tape so do not lift the scope ay off the bench, just rotate it so you can see
the underside and remove the protective cap from the undersurface and the objective
after that (see pictures below). You can now remo e the protecti e cap that was taped
across this bottom aperture and keep it to one side (this is a protecti e cap for your
eyepiece).
Step 7. Remo e the paper boat completely
and remo e the ‘ arious small parts package’
that is sandwiched in between the stage and
focus platform near the back (as shown).
Step 8. Take the parts out of the ‘ arious small
parts package’ and lay them out. Also remo e
the parts from the package containing the mirror
– these will be the mirror with its holder plus the
ocular lens holder assembly.
You are now ready to progress to assembling
the microscope as described below.
PUMA Foundation Scope Page 12 of 40 User’s Manual v1.0
Protective
cap

Assembling the Microscope
The following describes the recommended procedure for
assembling your Foundation scope for the first time after
remo ing all the parts from the shipping box. A ideo has been
prepared to illustrate this and can be accessed ia this link:
Step 1. First remo e any components from their separate bags / pouches and remo e
the ocular lens from its box (but keep the objecti e lens in its case for now)
Step 2. When the scope ships from OptArc the focus platform is fully raised so as to
accommodate the arious parts that are packed in between the stage and the focus
platform. This means the focus mechanism springs will be fully compressed so the next
thing to do is lower the focus platform a little to take some of the compression off these
springs. Do this by turning the coarse focus wheel a few turns as shown in the figure.
When looking at the scope from the top aspect this amounts to clockwise rotations of
the coarse gear. Don’t lower the platform all the way down. You will adjust correct
focus after the scope is fully assembled (as will be described later).
PUMA Foundation Scope Page 13 of 40 User’s Manual v1.0
PUMA Assembly Video
https://youtu.be/C-2 RsHi46c

Step 3. Turn the scope upside down and loosen the thumbscrews that hold the mirror-
to-baseplate attachment in place. Do not remo e these thumbscrews, just loosen them
enough so you can slide the mirror attachment into the slot between the baseplate (i.e.
the undersurface of the stage) and the mirror-to-baseplate attachment – as shown.
When inserted re-tighten the thumbscrews just enough to pre ent passi e wobble of
the mirror attachment but loose enough to allow rotation of the mirror attachment.
Step 4. Screw on the front two legs which ha e the plastic foot part pre-threaded onto
the metal spacer. Make these finger tight. For the back leg you choose whether you
want to use the plastic foot only – this will allow the scope to tilt backwards for ease of
manual iewing – or use a metal spacer + plastic foot combination (as you used for the
front legs) – this will make all 3 legs of equal height so help keep the stage le el (useful
if you are using fluid specimens or oil immersion). To make the metal spacer + plastic
foot combination first attach the plastic foot to the spacer (screw it onto the spacer all
the way it can go) so that it will look identical to the front two legs.
PUMA Foundation Scope Page 14 of 40 User’s Manual v1.0

Step 5. Insert the (empty) filters into the simple filter block. Note that the slots for these
two filters ha e no di iding wall between them so take care to insert each filter le el
and not at an angle to cross o er from one filter slot to the other. The filters must also
be inserted the correct way up – the marking on the filter handle must face upwards
(towards the ocular end of the optical tube) as shown in the figure. It is ad ised to insert
the lower filter first because you can use the base aspect of the filter block as a guide to
pre ent angling the filter upwards across into the upper slot. The top filter can then be
inserted and so the already sited lower filter will help pre ent angling the top filter
downwards:
Step 6. Screw the monocular tube into the top of the simple filter block by means of the
smaller thread on the monocular tube and make this finger tight.
Step 7. Screw the ocular holder assembly onto the top of the monocular tube.
PUMA Foundation Scope Page 15 of 40 User’s Manual v1.0

Step 8. Remo e the objecti e lens from its protecti e case and thread it into the thread
at the bottom of the simple filter block.
Step 9. Insert the ocular lens into the ocular lens holder – it is a simple push fit. This may
not be a tight fit so be careful not to invert the optical tube from no on or the ocular
lens may fall out and be damaged.
Step 10. (Refer to illustrations on next page). Now insert the completed optical tube into
the focus plate of the stage ia the quick release (QR) mechanism. The procedure
described here was designed to minimise the risk of crossing the thread of this
mechanism because forcing this in with a crossed thread could damage it.
First note that the final position of the optical tube, when fully inserted, is with the lug
on the simple filter block facing forward (the lug it is slightly off centre by design so
don’t be concerned about that) and with the filters and filter slots facing back towards
the focus gears (see picture). Howe er this QR fitting is a rotational mechanism so start
with the optical tube orientated 90 degrees anticlockwise so the lug on the filter bock
faces left (as shown) and lower the optical tube into its receptacle hole in the focus
platform till the tips of the three threads stop it going down any further. At this point
ensure that the optical tube is flat against the focus platform (i.e. fully perpendicular
to the focus platform, if the focus platform is tilted backwards then the optical tube
must be equally tilted – it must be perpendicular to the focus platform, not the work
bench). Now rotate the optical tube – while keeping it flat and le el – clockwise. If all is
well the optical tube tube should easily rotate and descend and click into place when a
quarter turn is complete. If you find you are requiring force you should un-rotate and
double-check to ensure the threads are not crossed (the ideo should make this clear if
the below diagrams are insufficient).
PUMA Foundation Scope Page 1 of 40 User’s Manual v1.0

PUMA Foundation Scope Page 17 of 40 User’s Manual v1.0

Releasing the optical tube from the focus platform is simply a matter of rotating it
anticlockwise.
The only thing left to do now is add a specimen slide and adjust the focus. These steps
will be elaborated in the next chapter because they are common to making
obser ations.
Filter slider trays and retention collars
The filter trays supplied with the Foundation scope are empty (they don’t contain any
filter) but they are the complete mechanism whereby you may add your own filter. Each
filter has a split ring filter retention collar. These can be kept separate or fitted to the
empty filter trays as you prefer (see below on how to fit them). You will need to remo e
these retention collars if you plan to add an actual filter to the filter tray at some point.
To add a filter, your filter must be able to fit into
the filter well in the tray without falling through
the well aperture. This means it must be round
with a diameter of 17 mm to 18 mm. Your filter
must be no thicker than 0.9 mm or the total
thickness of the filter tray mechanism once the
retention collar is in place will be too thick to go
into a filter slot in the filter block (you might get
away with thicker filters if you only use the lower
filter slot keeping the upper slot unoccupied but
then you won’t be able to properly retain the filter
with the split ring filter retention collar).
To fit the filter, ensure
the collar is out of the
filter tray, simply drop
your filter in the filter
well then re-apply the
split spring collar to
hod it in place. Note
that the collar MUST
be fit the correct ay
up because it is not
symmetrical. The wall
of the filter well and the
wall of the split ring
collar each ha e a complementary slanting angle to facilitate the collar’s retention in
the filter well (see picture of the cut-away CAD model abo e). To remo e a filter
retention collar you can use a needle or a tiny jeweller’s flat bladed screwdri er to
winkle it out of the filter well (taking care not to damage any filter that may be present).
If there is no filter present you may be able to pull the collar out with your bare finger
(no tools needed).
PUMA Foundation Scope Page 18 of 40 User’s Manual v1.0

Making Observations
How to place a specimen on the stage
Although arious types of specimen can be used this guide refers to the use of a
standard 25 x 75 mm glass microscope slide containing a co erslipped specimen such
as the test slide supplied with your PUMA Foundation scope.
Ensure the slide is the correct way up
(label and co erslip facing up) and put it
flat on the stage to one side of the
objecti e then slide it on the stage till the
specimen on the slide is approximately
centred under the objecti e. This
procedure is recommended to a oid the
danger of scratching the objecti e with
the slide – keeping the slide flat on the
stage at all times reduces that possibility.
Once the slide is in position place a stage
clip in its hole in the stage (these are the
holes closest to the front edge of the
stage) and press it down on the slide. It is
best to do it this ay rather than fix the
stage clip on a ay from the slide and
rotate the clip onto the slide because
that method ill create tiny glass
fragments as the metal clip scrapes over
the edge of the glass slide and this glass
dust is a health hazard and also could
cause scratches on your optical lens
surfaces over time. The online ideo
illustrates this safe method and how it
differs from the method to be a oided.
Note that the specimen slide could alternati ely ha e been inserted with the optical
tube remo ed. This is sometimes preferred, especially when using high power (high
magnification) objecti es. High power objecti es are physically longer than the x4
objecti e that is supplied as standard with the Foundation scope and so they ha e less
clearance space between the objecti e lens and the stage. This means there is a higher
risk of doing damage to the objecti e by touching it with the slide when inserting the
slide with the optical tube in place.
PUMA Foundation Scope Page 19 of 40 User’s Manual v1.0

How to focus the scope
You are now ready to focus the scope onto the specimen and begin obser ations.
Position the scope so that the mirror can catch reflected diffuse light (e.g. from a cloudy
sky) and, while looking down the ocular lens, hold on to one or more of the legs of the
scope and rotate the focus gear (fine or coarse) till the image of the test specimen
comes into focus. It is likely that, if you ha e followed this guide for assembling the
microscope, the focus platform will be too high and so will need to be lowered.
Therefore you can begin by rotating either focus gear in a clockwise direction. Due to
the elastic backlash of the mechanism you may need to focus just past best focus and
allo the backlash to take you back to best focus .
Coarse focus may be quite hard to mo e in some cases. If that is the case you can
perform all focus action with the fine focus gear – it will just take more turns to reach
your destination.
Attaching a camera
A camera or camera adapter is not supplied as part of the standard PUMA Foundation
scope package but with suitable additional equipment it is possible to take photos and
ideo using PUMA. OptArc can supply a range of cameras suitable for use with any
PUMA microscope. This section will gi e a brief o er iew of the use of three different
types of camera. Detailed instructions will be left to the instruction manuals supplied
with the camera or adapter equipment. Digital cameras require a computer and
software to record the image but for some (e.g. smartphones) the computer and
software are integrated into one de ice.
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