I am interested in building a OpenFlexure Microscope.
What is the diference between the
OpenFlexure Microscope and the
OpenFlexure Delta Stage ?
OpenFlexure Microscope: Fasteners & Illumination Kit also contain the neccessary parts for the
OpenFlexure Delta Stage?
I am interested in making a microscope for high resolution with Rasberry Pi and the Pi Camera.
In here it says
Any model will do for the Raspberry Pi but in in this page it says
8GB model not supported. I happen to already have a
Raspberry Pi 4 Model B 8GB so I don’t know if the one I already have is compatible or not?
Regarding the camera, my understaing is that we need the Raspberry Pi Camera Module V2. Would the Raspberry Pi High Quality Camera Module also work (without the lens mount)?
Thank you very much
The microscope and delta stage will both operate as high resolution microscopes. The main difference is in the configuration of the motion. In the Microscope version the motion has independent actuators for the three axes x-y-z. The stage is moved in x-y by two actuators and the optics module is moved in z by the third actuator. In the Delta Stage version the optics module is fixed and the stage moves in x-y-z, but there are not separtate actuattors for teh three axes. To move in z all three actuators must move together. To move in x or y two actuators move together and the third in the opposite direction. With motor control this calculation is built into the software if you select ‘delta stage’ in the settings, so you can just ask for motion in x, y or z as required. If you are moving by hand the Microscope gives the intuitive motion. The Delta Stage is in principle better for heavy optics as the optics are fixed rather than hanging on a moving actuator. Otherwise the optical performance is the same. The Microscope has the stackable bucket bases, so if you are wanting extra or non-standard electronics that gives a good way of housing them.
The fasteners and illumination kit is the parts needed for the Microscope version. The Delta Stage operated as a microscope requires most of the same parts. The optics modules, illumination and actuators are basically the same. The difference if any will be in the number and length of M3 cap head screws required.
I don’t know what is different about the 8GB Pi that caused problems, or whether that is still the case with the current version of the server.
The Pi High Quality Camera has a different sensor size and would require a different optical system. use the PiCamera V2. See this thread Support for HQ Pi camera - General - OpenFlexure Forum
The Delta Stage is in principle better for heavy optics as the optics are fixed rather than hanging on a moving actuator.
In theory, a variant to get the best of both worlds is to separate the light capture process from the CCD via a fiberscope arrangement … you’d have a lightweight lens assembly on the moveable optics with a short fibreoptic cable to a splitter prism for eye/capture which can be as rugged as desired. Conceptually this would allow upgrading of CCD or switching out for spectrum optimisation (eg fluroscopy) as budget permits.
Thank you both for your replies.
I started building the microscope version.
The documentation says:
If you printed the parts yourself, start by opening out the three holes in the microscope body with a drill as shown.
Is this a valid step for the current version of the microscope? I had the impression that the holes have already sufficient diameter and length.
What is the purpose of the two thin plastic supports that one needs to break?
Thank you very much!
The holes usually do print big enough, it depends a little on your printer.
The ties are necessary to hold the actuator column in place while it is printing. For the microscope to work the actuator needs to move so the ties must be cut.
Thank you, I have now built the microscope and I am very happy with the result.
I will now think about upgrading it to the High resolution optics module.
How do I know if this 2 objectives are RMS F50D13, or RMS infinity F50D13 or RMS F40D16?
Thank you very much
The F50D13 and F40D16 refers to the tube lens that you use in the high resolution optics module. 50mm focal length 13mm (half inch) diameter is what we usually use.
The ‘infinity’ or not refers to the microscope tube length that the objective is designed for. Usually the lens will say 160 or the infinity symbol somewhere. Those do not, which probably means 160mm, but you should be able to look up with all the details on those lenses.
silly question, since I know little about optics.
No mater which objective we use, we always need this lens, even if it is infinity corrected?
Yes. The lens is the same for different objectives. The positioning is different, so you have a different printed part to hold the objective, f=50mm lens and camera depending whether the objective is infinity corrected or not.
Is there a minimum objective magnification one can use?
I put a x5 and this is the best calibration I can get.
With higher magnifications I had better calibrations.
Also should the brightest spot of the condenser be focused on the sample or elsewhere?
5× has a big field of view and can be broader than the area illuminated by the LED with the condenser in place. You can see the image of the LED and its wires in your calibration image. Using a diffuser will help, and it is always best to diffuse the LED anyway. Use some fine sandpaper to roughen the LED slightly is probably easiest.
The other issue with low magnification lenses is that the movement is slow. The motors will translate across the field of view of 100× lens pretty fast, and in an acceptable time for a 20× lens. For 5× it is going to feel slow. The z-axis range will also be limited and the movement will be slow, for the kind of distances you are likely to be using with 5×.
Conceptually a simple way to have faster speed at the larger step size that you need would be to swap the big and small gears on the motor and actuator. Rather than gearing down a factor of two, that would gear up a factor of two. It would all fit, but the mounting at the centre of the two gear types is different so you cannot just swap.
By raising a lot the light source I managed to have a uniform illumination and proper calibration.
Now I have an unrelated issue.
I have lost the stream. When I open OpenFlexure connect I get
Restarting the microscope didn’t help
Also what does any of this mean: (I get this when I shut down the micrscope)
I have no idea what the first one is, it looks like the kind of thing where a restart would kick it back to working. As that does not work, try going to the command line on the microscope (either the desktop or SSH). I think there is a command
sudo ofm repair which you could try. Otherwise
sudo ofm update then
sudo ofm upgrade might help.
The second one basically means that it could not find the microscope (because it is off) and do you want to look somewhere else for it (the app does not know that it is just switched off).
Thank you, I managed to fix the issue when I saw this message in the log:
I had to reduce the bitrate from Max to High.
and have good looking images
When moving the stage, does the stage stay perpendicular to the camera/objective or does it tilt?
Just so I know how much one can improve the focus in the image above for example.
actually I am not sure if the focus is the issue
(distance between markers is 100 um)
I am actually having issues with the camera again
Setting this settings as below helped. But I am still getting some lines as below
Do you know what makes this happen? This is using OpenFlexure Connect
EDIT: is it possible to connect locally to the microscope by USB-C?
Really nice clear pictures for the one that works @pristinscope.
The broken up image does not look like a bitrate problem. The main symptom of high quality and a detailed image is that the full frame is not transferred and the app shows a blank white image. The image problem you have looks intermittent during the frame. The camera cables for the Pi camera can be quite picky. Make sure that they are well seated at both ends and that none of the wires could be cracked. The cables are not shielded, which is not usually a problem, but are there big sources of interference around?
The stage stays horizontal as it moves. There will be a very small amount of motion in z when the x-y actuators move, but there should be no tilt as the motion is based on parallelograms.
What could cause interferences?
Also, what could cause the left side of the image to be less in focus?
If the sample was tilted I would expect the opposite side to be out of focus as well.