More Lasertec C130 Notes

I’ve been playing around a bit more with the Lasertec microscope. Looking at the literature Lasertec microscopes are often described as “Semi-confocal” this explains the lack of a galvo or anything that I could see that would deflect the light in X and Y:

So I suspect that the silver box at the top of the unit is the AOD and the detect (which is after all marked “slit detector”) is a silt detector!

I decided to pull out the CCD:

And cram a different sensor into the vacated void:

This for taking epi-illuminated images, this works somewhat reasonably:

LaserTec C130 Notes

I was pulling apart an old LaserTec C140 confocal microscope. Here are some pics! Here’s the main optical block:

There’s a photodiode, I assume with a pinhole and CCD sensor here:

On the other side of the unit there’s an FPGA.

Under the unit there’s a stepper (right) and a BL55 “Laserscale”.

I’ve been trying to figure out how all this fits together. The unit appears to be white light only, but I’m unclear on where the actuation is. It looks like everything is on the bottom of the unit. I guess the BL55 laser scale is used in combination with that stepper. But I’m not clear if there’s a full sub-micron precision XYZ stage here or if there’s something else going on. I was really expecting to see Galvos to scan the spot across the sample… hmmm.

Arducam Pivistation 5 Klarity I2C

I was trying to interface directly with the I2C on the Arducam Pivistation 5 Klarity camera module for… reasons.

Anyway I figured this would just expose the I2C on the IMX283… but it doesn’t seem to. There seems in fact to be another little microcontroller (GD e230f8?) there which uses a different I2C command set. It seems similar to the interface from this camera:

https://github.com/ArduCAM/Arducam-Pivariety-V4L2-Driver/blob/7d49aa22558254cd415ef5bbca458a39ad130dce/patchs/arducam_driver.patch#L38

Anyway… I was able to get some info out of it using a Glasgow Interface Explorer. This note is here so someone else doesn’t waste time wondering why the IMX283 (which I think should respond on 0x1a) is responding on 0x0c on this camera.

The Glasgow commands required are below:

Also, it seems that you can crash the microcontroller pretty easily by doing additional reads?

Pacific Biosciences Accuracy Notes

DateOverallInsertionsDeletionsSubstitutionsRead LengthRef
PacBio RS II~2013~11%“predominantly indel”“predominantly indel”“predominantly indel”Vendor
PacBio RS II2020~13%8%3%1.68%Academic Benchmark
PacBio RS II CLR202012.88%8.04%3.16%1.68%8899Academic Benchmark
PacBio RS II Subread201714.2%5.92%3.01%5.27%Academic Benchmark
PacBio Sequel I CLR201912%Inferred from Vendor Claim
PacBio Sequel II CLR201910%~50KbInferred from Vendor Claim
Revio (Subread)202310%All: 100Kb+?Inferred from Vendor Claim
PacBio RS II CCS20171.720.087%0.34%1.3%1772Academic Benchmark
PacBio Sequel HiFi20220.25%0.1%0.13%0.02%Academic Note
PacBio Sequel II CCS20190.14%Academic Benchmark
PacBio Sequel  II HiFi2019<0.1%20KbVendor Claim
Revio (All HiFi)2023<0.1%16.5KbVendor Claim