Hi everyone,
I am a Canadian geologist with academia and industry experience. In my work, I collect a large amount of petrographic slides from surface samples. I have found that it is difficult to share information amongst colleagues that do not have access to a petrographic microscope. Common tools allow you to produce low resolution scans, or select high resolution photos taken with a microscope. My objective is to modify an OFM microscope to be able to scan the full surface of a petrographic slide in one or two sessions (46 x 26 mm) with a moderate magnification (10x). In order to understand the capability of the system, I have built an upright OFM v7 with no further modifications. Prior to making changes to the body to improve the stage range of motion, I wanted to share some notes from my build and also ask some question about the optics.
I have built the microscope over 3 evenings with no significant issues. I used TauLabâs Sangaboard and illumination system. Great communication and fast shipping. Highly recommended. Otherwise I used a raspberry 4B and the module 2 camera. I sourced the doublet lens from Surplus Shed (13 mm dia. 49 mm FL achromat doublet lens) and the nuts, bolts and Viton rings from McMasterCarr (USA). Here are the mistakes I made during the build:
(1) I broke one of the hinge of the flexure system, on the stepper motor side, when trying to fit the nuts in the stage but did not notice it until I had assembled the mechanical parts. This essentially limits the effective range of one of the axis. I had a spare body so I quickly re-traced the building steps the next day.
(2) I ordered a 30 cm pi-camera cable but it is too short. You need at least 50 cm for an upright build with an infinity corrected module.
(3) I connected the led module to the wrong port. I found the best information about where to connect the led module on the Sangaboard is on the forum. I would suggest adding a photo to the instructions.
(4) I used the monitor port to connect the camera on the Raspberry pi. Easy fix.
(5) For an upright build, the camera should be rotated 90 degrees to match the X-Y axis on the software. It is easy to generate a modified STL on openSCAD and I will print a new module to fix that.
I was not expecting the build to go that smoothly. I was equally impressed with the software and its scanning capability with autofocus. However, I believe I did not print the appropriate optic module for the microscope lens that I am using. I am using an Olympus MSPlan 10x/0.3, infinity corrected with a mechanical tube length of 180 mm. It is a good quality lens (low aperture of 0.3) so I would expect it to be quite sharp and have a good depth of field. I have not tested it on a commercial microscope.
The focus quality is reasonably good in the middle of the image but decreases radially so that most of the photograph is slightly out of focus. I have used the âoptics_picamera_2_rms_infinity_f50d13.stlâ file to print the optic module and I believe the sample is reasonably flat. There is a slight misalignment between the light source and the lens which produces a dark halo in the upper left corner but that doesnât seem to impact the focus quality (all corners are equally out of focus). See the following pictures:
Plane polarized photograph of a partially chloritized (green) biotite grain (brown) surrounded by a quartz and plagioclase matrix (colourless).
Cross polarized photograph of a biotite grain (dark brown) next to a plagioclase grain (grey) with some basal twinning (different shades of grey along the grainâs long axis)
Edit: I also took a photograph of a business card with reflected light (Ikea office lamp!) to provide an homogenous pattern to better visualize the focus quality:
I had a look at the openSCAD parameter files and attempted to generate another optic module for an infinity corrected lens with mechanical tube length of 180 mm. I noticed a difference between the initial model I sourced from the website (green module in image below) and the one I generated (yellow modules) but no difference between models for an infinity corrected optic module with f=160 mm (centre) or f=180 mm (right).
I also had a look at the optic design page and noticed that the change of mechanical tube length from 160 to 180 mm should impact the focal length of the achromatic lens used to focus the image on the camera (from 50 mm to 63 mm). Does that mean I should be using the same optic module but with a different doublet lens?
Edit: After some extra reading I now understand that the mechanical tube length may not matter for infinity corrected lenses and that the focusing distance of between the sensor and the tube lens is what really matter. Adding to my confusion, I measured on the STL file and all optic modules in this photo have a distance of 49 mm between the seat of the doublet lens and where the the surface where the camera module gets sandwiched (where the breadboard sits) so the sensor should come short of the required focal length. Would that explain why my camera doesnât focus perfectly? Meaning that the image is always in focused a few mm behind the sensor? ( Assembly Instructions (openflexure.org)
I hope this will help other people to build their microscope and that someone will be able to help me with my optics issue.
Cordially,
Nicolas