Raspi and camera modul

Hi, thanks for the forum that u created
is that possible if we use Raspi model 5 and camera modul PI version 3 for the microscope

Welcome to the project @abt34. Currently the only camera that is supported in the software (Openflexure server version 2.11) is the raspberry Pi camera v2.1 and the only main boards that are supported are Raspberry Pi 3 and 4.

This is entirely for software reasons on the version of the camera control library that we use. The library allows the colour correction and fast autofocus which are two of the main enabling features for a robotic microscope.

@r.w.bowman is currently undertaking a complete rewrite of the software to use the current Raspberry Pi camera library and also to make many other improvements. This will be the server version 3 and is not yet ready for release. It should be able to support a wider range of cameras and will work on the Raspberry Pi 5.

For now we are tied to the Pi Camera v2.1 and Pi 3 or 4, which work very well in the microscope.

thank for the answer, and how about the hardware, its still need a improvement or same

Variations of the parts to fit other electronics are relatively straightforward to do. To avoid any confusion these will not be implemented until the new electronics are supported by the software.

I am sure that this might be the case but want to ask before having to buy another pi camera. Does this mean that pi camera V2.0 is not compatible in software but V2.1 is ?

I don’t actually know of any 2.0. Many retailers simply say “version 2” but all the cameras that I have seen have 2.1 on the board in images on their websites. Camera version 1 (marked 1.3) certainly does not work.

Edit: It looks as though camera V2 was indeed v2.1 at launch.

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can we make the microscope just only 2 coordinates XY without Z coordinate

The short answer is Yes.

Could you say a bit more about what you are trying to do? In the microscope the optics are mounted on a separate translator from the sample stage, so the x-y motion is physically independent of the z motion. You could install the screws, bands and motors only on the x and y actuators for x-y motion. In fact the underlying design code builds the parts separately, so from the source SCAD you can switch off the z-axis and the illumination mount to make just an x-y stage. You were talking about the camera as well, which would need z for focus in a microscope configuration. If you just meant that you only want to motorise x and y but not z, that is just a matter of not including the motor on z.

This is an example of an x-y version of the stage with the z-axis parts not built.

what I want to do is only make a microscope with xy coordinate motion. so the z coordinate will be stationary. so the automatic system is only for xy motion. thanks for the answer, and where can I get a 3d file that I can edit myself, or there is already an stl file for xy only.

If you want the z-coordinate stationary, but the z mounting position to be present, then that requires the standard microscope body with the z actuator blocked. The easiest way to do that is to just add a couple of cubes or cylinders in your slicing program that overlap with the internal mechanism of the z-axis. You just need to check in the sliced layers that it does hold the mechanism without changing the dovetail optics mount or getting in the way of the access to the mounting screw for the dovetail.

For a mechanism with x and y only but no optics mounting position, as in my photo, the best thing is to go to the Gitlab Repository OpenFlexure / openflexure-microscope · GitLab. This has all of the design files in the openscad directory. You would need to download all of the files (the blue code button at the top right gives you clone or download options). Then using OpenSCAD 2021 (open source) you would want to edit the file main_body.scad. In line 29 near the bottom you would change the line

   main_body(params, version_string);



then use OpenSCAD to render (press F6) and create an STL (press F7). You might find that the OpenSCAD preview will fail, but you should be able to render.

(The detailed code for the main body is in \libs\main_body_structure.scad if you needed to change anything else)

thanks for your answer and information its very helpfull for me, by the way if the z axis will be stationery then what happens to the way the microscpe works, whether it affects the focus of the camera lens or does not affect the way the microspce works.

If the z-axis is completely fixed then you have no way of adjusting the focus. If you are using a lens and camera that are on the microscope then you will need to have the z-axis working to get the sample in focus. The stage is very stable, so once it is in focus the sample will not move much. Using a 20x lens or the ‘low-cost optics’ version of the microscope you may not need to re-focus even for long periods (~ a day) as long as you don’t move the sample in x or y. If you do move the sample it will need to refocus after some movement, depending on how flat and straight your microscope is. With higher magnification versions of the optics the depth of field is very small, so even the highly stable microscope stage is likely to drift out of focus over a period of minutes/hours, and you will certainly need to re-focus if you move in x and y.

The only times when it is helpful not to have the z-axis moving would be if you had the stage as part of a system where the focusing is done by other parts of the system.

If you are actually mounting something inside the stage - like an upright illumination module - I would just print the Z axis and just not put a motor on it. That way you can still fine tune the distance by turning the gear by hand. If you are using epi-illumination I would still print the z-axis that way as you can fit a bright field illumination later.

If you have the whole thing on a rail with 3rd party optics and illumination adding a z-axis for the - probably much inferior - OFM illumination is not of much use. But you sound like you want to use a OFM optics module. How do you want to focus at all? You will need to focus somehow.

Hi William.

Thanks very much for this info! I’m wondering if there are any updates on the status of the new software?

I foolishly recently bought a bunch of version 5 main boards and version 3 cameras in preparation for a course I’m hoping to run in Senegal around November/December and realised the problem when I got to test building.

Server version 3 is progressing, but not ready for release yet. The first release will still probably only support Pi 4, although it may support more than just camera v2. I am not familiar with the inner workings of the server, but I gather that porting to the Pi 5 needs more changes than enabling different camera versions does.
That said, there is quite a lot of time until November.