First Cam Field Test – 5th July 2016

First Cam Field Test – 5th July 2016

It’s always an exciting day when you take your prototype into ‘the field’ for the first time. Although things may be working well in the lab, you never quite know what will happen when you take them into the real world!


We had decided that it was time for us to venture out and conduct our first field trial. As we had strong suspicions that the River Cam would be harbouring a few(!) bacteria, we thought that it would make an excellent first test, not least because we could then sit in Jesus Green and enjoy an ice-cream and BBQ at the same time!


We collected a sample by Jesus lock, and were surprised by how clear the water was. However, the first round of filtering left a very dirty filter, showing just how much particulate matter can go unseen in the water! We then filtered the water again to catch any bacteria, and transferred the bacteria to agar. So far so good (especially as the sausages were nearly ready...).

cam riveralex and Nalin


The agar plate was then placed on the microscope, allowing us to test our new incubator. Unfortunately, a few burgers and an Old Speckled Hen later we couldn’t see any growth using the microscope. It was a disappointment, but it was to be expected that something wouldn’t work first time - we just had to work out where the problem was!


waterscope team at camben and richard

Thankfully, after leaving the agar in a commercial incubator for a short while we were able to see growth down the microscope. This suggested that it might be that our incubator isn’t working as effectively outside as we had hoped. Now back to the lab to tinker with our incubator ready for our next field test!

cam river trial result

Using “proper” microscope optics with the OpenFlexure Microscope

Using "proper" microscope optics with the OpenFlexure Microscope

A commonly-asked question when I speak to people about the microscope is "can it do X?" for various different values of X.  Often my answer is that, while the basic model I'm showing you here can't, I have another version that can.  This blog post is about the other versions, and how to get hold of them.  First though, I'll list a few of the most commonly asked-about features:

  • Better resolution/higher magnification
  • Wider field of view
  • Use of a "proper" microscope objective
  • Imaging modes other than bright-field (e.g. dark field or phase contrast)
  • Fluorescence imaging
  • Motorised control of the stage position and focus
  • Upright geometry (looking down on a sample rather than looking up through the coverslip)

All of these things have been done with the microscope, pretty successfully.  however, not all of them are available easily.

Writing good instructions is hard, and despite putting a lot of effort into our instructions, it's still very easy to confuse people.  This is particularly problematic when there is more than one way to do something; experience has taught us that it's easier for everyone to pick a method and stick with it.  However, this makes it hard to include optional features, which usually affect one of the assembly steps in some way.  Consequently, I usually encourage people to get in touch if there's a feature they want, so I can point them in the right direction.  I'll save most of those features for future blog posts, but I'll add the instructions here in case anyone wants to use a real microscope objective instead of the Raspberry Pi Camera module's lens.

Better resolution, higher magnification, and wider field of view are all possible if you use a "proper" microscope objective.  There are designs on GitHub for a modified optics module that takes a 40mm focal length planoconvex lens and a conventional RMS-threaded microscope objective.  The "Large Stage" version of the microscope is needed to accommodate this (the small stage is not big enough to fit the larger objective into), and it in turn requires a different illumination arm.  The bigger microscope is denoted by an "LS65" in its filename/model number, meaning a wide stage that is 65mm high in total. I try to keep the STL up to date for those who don't have OpenSCAD, but the most up-to-date version will always be the OpenSCAD file; in microscope_parameters.scad you need to set "big_stage=true" to get the large stage version.  Then, open and compile main_body.scad to generate the microscope and illumination_and_rear_foot.scad to make the illumination.

We've settled on a 40mm focal length, 16mm diameter lens for the inside of the tube - this is necessary as otherwise we'd have to use the microscope objective at the wrong working distance.  I get ours from Comar - the 40 PQ 16 works nicely.  You should be able to push-fit the lens, and essentially push fit the objective too, though we usually screw them in to avoid crushing anything.

If you've tried this recipe, or if you'd like us to sell you a custom kit for it, do get in touch!