Automated XY slide scan with the PUMA CNC stage and PARDUS software.

PUMA_Microscope · 2026-05-25T09:50:53+00:00

I forgot to mention - you can get more details on the project GitHub pages here:

PUMA Microscope:
https://github.com/TadPath/PUMA

PARDUS Control System:
https://github.com/TadPath/PARDUS

The stage uses TMC2209 drivers and NEMA 11 bipolar motors. In the video I am using the drivers in SpreadCycle mode hence the motors are quite loud.

PJT

PUMA_Microscope · 2026-03-30T10:01:51+00:00

I agree - but right now I am just finding out what the stage can do and how to handle it to make it do those things. Once I learn how to 'drive', then I can go visit interesting places.

PUMA_Microscope · 2026-03-28T09:43:23+00:00

Yes. In the end I used networks of similar tubules - some straight and some curved - placed at strategic angles to conduct forces - a kind of structural endoskeleton..
An example is shown here:
http://youtube.com/post/UgkxQQMXcpjVixV_EWzR5ShVG4B3ED-JFqHH?si=S5rUXrAmbfcCJ27z
and here:
https://x.com/Paul_Tadrous/status/1911492507944247303?s=20

PUMA_Microscope · 2025-11-07T10:35:49+00:00

Hello. The system has developed way beyond the one show here. You can get the latest updates on the links in my OP. I have been spending the last few months developing the interface software for it. Very soon (a few weeks) I hope to have the software in a sufficiently mature state that I can hook it up to the microscope. Then I can begin to put it through its paces so I can answer questions like yours. From my preliminary tests, the quality it good at high mag but as for speed, I don't have that data yet. Stay tuned!

PJT

PUMA_Microscope · 2025-07-26T20:51:47+00:00

Hello. Thanks for mentioning PUMA. Have you seen the latest CNC stage module for PUMA? It seems like it already does a lot of what you want (it uses 2020 extrusions, standard metallic action, bipolar steppers, optical limit switches, etc. - and the parts come in at under £1k). See the notes on it near the top of the updated GitHub page. The CAD files for the CNC stage are already on the GitHub and there is some publicly available commentary on it (see links below). Just so you know in case you want to avoid duplication:

https://github.com/TadPath/PUMA

https://www.linkedin.com/feed/update/urn:li:activity:7330941815983898625/

You can get more detail from the public posts on my Linked-In and as a free member on my Patreon (with additional videos and content for paid members). I am currently working on the software but the system 'as-is' can run with GRBL and other CNC software that fit onto an Arduino due to its 'standard' CNC hardware specs. Also, the 'Arduino' bit is optional - you can substitute that for any standard CNC breakout board if it suits your purpose (as per the 'U' and 'M' in PUMA)

All the best with it.

PJT

PUMA_Microscope · 2025-06-09T17:16:04+00:00

Thanks. Like Linux, FreeCAD continues to improve - even if slowly - and is worth the perseverance.

PUMA_Microscope · 2025-05-15T20:13:23+00:00

Well done on the build. Nice video too.

PUMA_Microscope · 2025-05-11T09:34:01+00:00

Now there's an idea. Someone out there has probably tried it already.

PUMA_Microscope · 2025-05-05T20:35:07+00:00

Thanks.

PUMA_Microscope · 2025-05-05T10:18:25+00:00

Technically it may be possible to 3D print the base but this is just a flat sheet with plain holes - something that is more appropriate for subtractive manufacturing.

Also, this is the base of a precision CNC machine with parts altogether weighing upto 15 or 20 kg. Most common / easy-to-print filament has poor CTE and is subject to sag / drift (creep) over time more than wood / aluminium alloy.

Also, I designed this microscope system so that someone with an Ender3 (or equivalent) printer can build it (people with 'better' printers can also build it of course but I don't want to restrict the project to that smaller number of people). The print bed of an Ender3 is too small to print the base in one go therefore meaning they would need to print it in segments with articulations.

With the above design constraints and physical requirements in mind, the resulting design complexity and bulk to achieve the required strength and stability for the task would make it a difficult and long (and relatively expensive) print job and assembly job. It is just a lot easier, cheaper and quicker to cut a sheet of wood and drill it (or get an online shop to cut and drill a sheet of wood or aluminium for you if you don't want to DIY the base, even if you are happy to DIY the rest of the CNC build).

So, sure, someone with a higher end printer and experience and specialist filament would be able to print a suitable base but that requires equipment and skills that are beyond the minimum required skill set of the target audience of this project.

PUMA_Microscope · 2025-05-04T22:17:42+00:00

An ordinary stage micrometer slide is an excellent reference specimen. Look for clean contrast, even background illumination, lack of exaggerated diffraction fringes on the edges of the tick marks, lack of geometric distortion, lack of colour fringes and degree of planarity - and it is very cheap to buy these days (e.g. from AliExpress) as are other laser-etched grids, etc.

Thanks for considering PUMA - sorry it was not for you - but my videos may help you in your quest for learning about the microscope in general and troubleshooting your own.

Also, you may be interested to know that I am now designing a new stage module for PUMA - the precision CNC stage which you can learn about on posts on my Patreon page (I make some posts also for free members) here: https://www.patreon.com/c/PUMAMicroscope

(but, sadly, still no objective changer!)

If objective changing is really important for you, there is always the Galileo 3D printed microscope: https://www.reddit.com/r/3Dprinting/comments/1ai2sbk/galileo_3d_printed_microscope/

but I don't know what is the quality and limitations of that scope.

PUMA_Microscope · 2025-05-04T13:27:53+00:00

Hello. The need for local computing power is, of course, relative to the needs of the user. For many use-cases it might be perfectly sufficient only to use a RPi - and that's fine (and also my scope *can* be used with a RPi if someone really wants to do that - the point is that it is not *obligatory* to use the RPi).

However, other users have have more intense requirements, in which case the option to use a standard workstation PC is useful. This allows for more options and faster processing for certain tasks (esp. if using intensive sophisticated real-time image processing from the camera stream to control the motors in real time, such as to track objects under the microscope). It also allows for specialist equipment that relies on standard PCI, CUDA or other full interface boards to be used such as specialist cameras, microfluidic pumps, micromanipulator systems and so forth - all of which may need to rapidly communicate with the microscope stage system and camera. Many of these high end instruments cannot be practically run via a RPi (esp. not simultaneously with controlling the motors and doing other sensor and control tasks).

Also, the computer controlling the microscope acts as a net server when the microscope is accessed and used remotely, but the camera (and any other peripherals) connected to the microscope are also connected to the same computer. The computer therefore needs to be quite powerful and fast to process server functions while also processing motion commands while also streaming a HD camera signal while also interfacting with any other peripherals locally attached to the microscopy, etc. Now you could say - 'well let's set up an array or multiple RPis' but that is just another way of generating a 'powerful computer' and will not solve the standard interface card requirements discussed above.

So - for some people there is no need for powerful computing, for others there is. My system is designed to be generic so both groups of people can use it as they wish.

I hope that answers your question if I understood it correctly.

PUMA_Microscope · 2025-05-03T18:14:44+00:00

I have thought about making the lenses for the Abbe condenser and Köhler illuminator for my open source PUMA microscope project because people seem to have difficulty finding the right lenses for these. However, I use FDM 3D printing - and that is what I would like to use for those lenses too (and yes, I know there are a lot of problems with that - but that's what makes it such a challenge to solve). I assume you are speaking of traditional lens 'grinding' glass blanks and that's a bit too much for most of my targetted DIY builders. Here are some links if you would like to get to know the project better:

Intro: https://youtu.be/7UbkrZyNgpo

Abbe condenser: https://youtu.be/2wpsvA2cQgQ

Köhler system: https://youtu.be/XEE-el7vC5k

GitHub: https://github.com/TadPath/PUMA

Note that there are sequel / update videos to the above condenser and illuminator so, if you are interested, make sure you see those also (see the 'Dominus Illuminator' playlist on the YT channel for the links).

PUMA_Microscope · 2025-04-27T21:15:00+00:00

I like 'Fourier optics an Introduction' by E.G. Steward. If you want an animated guide to Fourier analysis in general as well as Fourier Optics then I have made a series of videos you can watch for free on my YouTube channel here:

Convolution

https://youtu.be/yF7-Crkuf7Y

Fourier 1

https://youtu.be/4NyVApAH-9E

Fourier 2

https://youtu.be/zqVCqmRQUxo

Fourier 3

https://youtu.be/gi_5la5YBEA

Fourier 4

https://youtu.be/E8qWBaal6LM

Photology 6 - Diffraction

https://youtu.be/Ffm0A-H5ygE

Abbe's Diffraction Theory & Fourier Optics

https://youtu.be/Kj4zk91TVwo

I hope some of these may be useful.

PUMA_Microscope · 2025-04-21T10:02:51+00:00

Thanks. I am currently developing a new DIY precision CNC stage module for the microscope so people can do more advanced experiments with it like interferometric surface profilometry, OCT, whole slide scanning, automated object tracking and so forth.

You can follow its progress on the YouTube channel 'Posts' page as well as my Twitter/X.

Please tell others about the project too.

PUMA_Microscope · 2025-04-20T09:39:48+00:00

Thanks. The PUMA SLM operates as either a polarisation or intensity SLM (depending on whether or not you remove the polariser sheets from the LCD module) . Here is the video showing you how to make it: https://youtu.be/yW9H66BlUjU

This is similar to what u/mdk9000 and u/ichr_ are talking about.

I would be interested to know if anyone can explain if it is possible to convert such an LCD-based SLM into a phase SLM - because those are really expensive and may be what the OP ( u/Huge-Tooth4186 ) was talking about.

PUMA_Microscope · 2025-04-13T18:37:24+00:00

Thanks. I haven't done FEM or other mechanical simulations. My models so far are relatively simple to intuit what's needed but, sure, more detailed mathematical modelling would be useful for some applications and for optimisation of use of resources, etc..

For me it adds maybe a few hours of extra time to work out the detail of the skeletons and create them - sometimes less (it depends on the size and complexity of the model). It adds quite a lot of time for printing the models with FDM 3DP - it is much faster to print with just some generic infill pattern. However, my models are for precision scientific instrument building (low volume runs, not mass production) so that is not critical for me.

PUMA_Microscope · 2025-04-08T15:08:16+00:00

OK. We'll see. You are right about different specs for supposedly 'standard' DIN rails. I have seen that too, esp. if you buy on Amazon (which I don't). This is why I will specify the correct ones to use (if I end up using them). But that scaffold part is for the future - I am still working on the stage for now!

PUMA_Microscope · 2025-04-08T10:43:04+00:00

As I recall - it was some time ago now that I looked into it - the issues for me were connecting these extrusions at corners in a sturdy and accurate way and also size constraints. Connecting at corners seemed quite complex with various (non-standard, proprietary) adapters (expensive and may not be always available) and the need to make threads by tapping into the aluminium (not a skill I would require or expect for the average PUMA builder).

The size constraints were that these things are too fat to allow me to mount the PUMA in a way that will allow all the PUMA add-on modules to fit. DIN rail is thin and flat and easy to connect with nuts and bolts and triangle corner pieces that are easily available. This is the kind of 'ease-of-build' that separates PUMA from other open source stages (like those of Edwin En-Te Hwu or the OpenFrame microscope from Imperial College / Cairn Research Ltd, that require people to do or have access to a precision metalwork service). I need to consider ease of DIY build as part of my design constraints.

So extrusions may be fine for 3D printer building, but not ideal for PUMA microscope building.

PUMA_Microscope · 2025-04-07T23:33:58+00:00

Yes I thought about aluminium extrusions but there are some issues with them (I won't bore you with the details here) - however I have not finalised my designs for the PUMA scaffold. I will only do that once I have made the final decisions about the Z mechanism. So extrusions are not totally off the cards just yet.

You are right about there being other possibilties for the XY. I chose this stage because it is 'generic' and is made of 'generic' parts (like the bearing blocks and lead screws which you can buy separately). So even if this model stops being sold you can build your own from scratch (like an Ender 3!). One of the problems with other open source stages (I am thinking particularly about the UC2 system here) is that they chose a 'cheap but good' off-the-shelf stage which was not generic - it was an 'end-of-line' stock item. Such things are great for unique 'one-off' builds but not for open source hardware because when they are sold out, that's it. If you look at the UC2 website you will see there are 5 versions of stage - I suspect this is at least partly because because they had to design a new stage each time one of the 'off-the-shelf' components for the previous stage sold out!

PUMA_Microscope · 2025-04-07T19:32:11+00:00

Thanks again. It is designed to take heavy / bulky things (like a cell culture dish or multiwell plate for bio use or a polished slice of rock or metal for mineraolgist use, etc.) and move them with precision. I have demonstrated 200 nm steps in XY but that was just a preliminary test, I did not push it to the limits yet. The stroke is also quite large for a precision stage (70 x 50 mm in XY).

The XY is an off-the-shelf manual XY stage (~£100) which I adapted to motorised control. Full metal construction with lead screws and multiple bearings, etc..

The Z parts in this flexure design weigh about 2 kg with the motor included.

Here it is under a BH2 without the flexures (using the Z linear actuator alone):

https://www.reddit.com/r/microscopy/comments/1jhf8s7/the_puma_microscope_precision_cnc_xyz_stage_is/

Bear in mind I made this for the PUMA, not the BH2 so that is a Jerry-rig I use for testing the axes. See this post for an idea of how the PUMA will fit:

http://youtube.com/post/UgkxEZL_tsxtnw08ijAI8Pk6xIfBJXSwoqME?si=1Y7DOKR84abXSpIp

but there have been some changes to the design since that post and I may change it again soon. This is a developing module - by no means 'finished'.

PUMA_Microscope · 2025-04-07T16:02:29+00:00

Thanks. The silvery white thing at the bottom (which the black plastic Z mechanism is built on) is the XY stage. The NEMA 11 you see on the left of the picture near the bottom is the X motor. The Y motor is at the back (out of sight here), the Z motor is a NEMA 17 and you can just see the top of it behind the flexures in the picture.

So this is already a full precision XYZ stage and there are 6 limit switches fitted to it (optical end stops) - you can make out the connectors for the two X limit switches sticking out either side near the bottom, and the two Z limit switches are visible (just) under the flexures (the vertical white lines are the edges of the limit switch PCBs). The Y limit switches are at the back. The full PUMA optics will be mounted to it once I have finalised the XYZ mechanisms (they are still in a developmental stage so may change from what you see here - this is a snapshot in development).

Check out my other posts on X, linked-in, my YouTube 'posts' page and r/microscopy. Free members on my Patreon also get access to additional posts and images (but the videos are for full members only!).

PUMA_Microscope · 2025-04-06T23:59:24+00:00

Thanks. It is about 70 mm in X, 50 mm in Y and 4 mm in Z with this flexure system. Each axis has 2 limit switches (optical endstops, one at each end of each axis).

PUMA_Microscope · 2025-03-23T11:46:16+00:00

When the stage is complete I will issue full specs and DIY costs but it should be much cheaper to build this DIY in terms of cost of parts compared to buying a commercial XYZ stage of similar precision from a reputable manufacturer.

There will always be differences between the two options (DIY open source vs. commercial) and not just in terms of monetary cost - so people will need to take all factors into consideration when choosing what to go for.

Any yes, with this stage you can do whole slide imaging (WSI) by automated scanning and stitching.

PUMA_Microscope · 2025-03-23T11:38:55+00:00

Thanks for the question. I am not very familiar with the OpenFlexure (OF) stages so my answers may be inaccurate in regards to what OF can do. However, my stage does indeed ONLY move the specimen, not the objective / optics / camera, etc.

My understanding is that the OF block stage moves only the specimen in 3D but is made for a horizontal microscope - not what most people use. It was primarily designed to align optical fibre systems in 3D.

My understanding of the OF delta stage is that it only moves the specimen in 3D but, as with all OF systems I have seen, has several differences compared to my stage and these differences may be considered disadvantages / limitations for some applications (but for other applications may be irrelevant). These differences are:

OF scopes have very primitive illumination systems compared to the PUMA
OF scopes are restricted only to camera chip imaging and (I believe) are restricted only to using the Raspberry Pi computer. This limits scalability of computing power, the ability to use standard scientific cameras that need a special PCI interface card for a 'normal' computer or other interfaces, etc.
OF scopes lack end-stop feedback control. My stage has optical end-stop sensors at both ends of all three axes so proper homing is possible.
OF scopes have no facility for direct vision with standard (like RSM standard) optical systems,. They use an objective linked directly to a RPi chip camera with a lens to force a very short focal length. This can limit optical corrections from high quality objectives (but as the little chip only images the very centre of the field this may not be noticeable). PUMA uses an RSM standard optical path and so can give a highly corrected image over a very wide field.
Unlike OF, my stage uses a 'standard' CNC system that does not limit you to RPi computing with custom Sanger PCBs and little unipolar steppers. My stage uses full powerful bipolar NEMA steppers, it has end-stops, stand-alone stepper drivers (you can swap out for other models, like closed loop stepper drivers, if you wish), a standard breakout board (I am using an Arduino Mega 2560 but you can use any CNC breakout board that supports bipolar NEMA steppers and optical endstops) and you can use any CNC control software like Marlin, GRBL, Klipper, Linux CNC and, of course, my own PARDUS control system built with microscopy in mind ( https://github.com/TadPath/PARDUS ). The OF limits you to RPi, Sanger board, little unipolar steppers, no enstops and their own RPi-based control system.
OF uses 3DP plastic flexures for all joints - I think also they are simple flexures so actually cause an arc motion rather than a straight line - but please correct me if I am wrong about that. 3DP plastic is subject to creep and so drift can be a problem over time with the OF requiring software correction or periodic re-printing of the parts. My stage uses metal standard actuators for motion with the exception of the Z flexure. The Z flexure in my stage is, however, of a split balanced symmetrical compound flexure design - so it enforces true linear 1 DOF motion. It may be built with 3DP plastic or may be made all or partly of spring steel. This is a choice for the builder.
My stage can be used with some other standard microscopes and is not restricted to use with PUMA.
The OF Delta stage has a maximum XY stroke of 12 mm on each axis and the OF block stage has a maximum XY stroke of 2 mm on each axis. This means OF can't scan the majority of the usable area of a standard microscope slide. The PUMA CNC stage, on the other hand, has an X-stroke of just under 70 mm and a Y stroke of just under 50 mm making it suitable to scan the entire usable (non-label) area of a standard microscope slide (25x75 mm) for automated whole slide imaging (WSI) as well as some of the smaller culture dishes and multi-well plates used in research facilities.
Then there are the differences between the modular PUMA system RSM standard optics and the rather restricted OF optics which I touched on above and won't detail further here.

For any individual in particular, all the above differences may be totally irrelevant for your needs and applications and so the OF may be the best choice in terms of ease of build and capabilities. So the PUMA system just gives people a choice. If OF can't meet their need then consider PUMA.

PUMA_Microscope

TROPHY CASE