Illumina Patterned Flowcells Imaged!

Some time ago Graham Wiley sent me an amazing collection of flow cells. I’ve been sitting on these for a while for various reasons, but not least because the only patterned flow cell I could optically image was the HiSeq’s. Features on the NovaSeq and other flowcells were just too small to be seen with a regular optical microscope.

This meant it was probably time to go pick up the electron microscope from the farm and drag it down to my new “office” (1970s house). Predictably the microscope was dead. But today a very dodgy looking package arrived from India containing an oil covered turbo molecular pump and controller. This was the part I needed to get the electron microscope back up and running.

So! With the microscope barely alive, I decided I had to grab some images of the Illumina patterned flowcells in Graham’s collection. The images are not great, and the microscope likely needs better vibrational and electrical isolation. But to my knowledge these are the first public references which clearly show the feature sizes used on these flowcells.

As I’m indebted to Graham for the flowcells, this isn’t a paid post (please subscribe if you can it will help keep the SEM alive :)).

Thoughts

The easiest thing my sleep deprived brain can think to do is grab a square micron from each flow cell type and see how many wells we have in each. Doing this we go from 3 on the Hiseq to 4 on the NovaSeq and 8 on the NextSeq (shown above).

This is already a surprise as my assumption was that the NovaSeq had the highest flow cell density. However the NexSeq has double the density of the NovaSeq!

Perhaps this higher density technology is what we will see on the NovaSeq X!

Eyeballing it, it look like we have between 250 and 300nm between wells on the NextSeq, which is inline with my previous estimates. NovaSeq 6000 wells seem to be at ~500nm spacing.

Wells are almost certainly perfectly regularly, but the limitations of my current setup make them appear irregular, particularly at higher magnification.

That’s all for now! But there will be further posts with better images soon.