Raman has no reflection in the (dichroic) mirror

So I got tired of trying to align the little prism you can’t see in this picture (The one sitting between the microscope objective and the optical fiber assembly):


It’s been replaced with a 540nm long pass dichroic mirror:


And from above:


And finally with a 532nm laser pointer shone upon it:


It’s not perfect. The reflection is not quite 100%, and it is going to cost me on 10-20% of the intensity of the Raman scattered radiation. Hopefully the improved alignment will make up for some of this.

The system now more closely resembles a commercial Raman probe:


Tired of pi – try UART

The first functional UART-enabled firmware and GUI is ready.

You can now run the Otterly CCD GUI directly on your computer without the need for that annoying little rpi. Downside is the speed. UART is app. 150x slower than SPI.

So why bother with an even older and simpler communication protocol than SPI?

Well for now there’s no good reason except you save yourself the trouble of having to connect the rpi and nucleo. The real reason to go with UART is that without a master, the MCU can now decide when to transmit. This may not seem like a big deal – and it probably isn’t – but I haven’t been able to reliably do timed reads of the CCD using SPI. This will change (someday soon).

For downloads and slightly more info goto: tcd1304.wordpress.com

A waste of time

While it was “fun” to destroy a quartz cuvette and bring it back to life, it was also a complete waste time.

The point of the whole operation was to bring the focal point of the microscope objective inside the sample volume by reducing the wall thickness of the cuvette from 1.25 mm to 0.75 mm.

The microscope objective has a working distance (WD) of 1.0 mm in air, which means that the WD is >1.0 mm in any medium with a refractive index >1.

I’ve tried to photograph the focal point:

The images show fluorescein’s emission by excitation with a 532 nm laser. The spectroscopic cell has a wall thickness of 1.25 mm. The difference in the illumination angle is due to a difference in the diameter of the collimated laser light entering the microscope objective.

If you really want you can sort of persuade yourself to see that the light is focused just inside the spectroscopic cell. If you’re more of a sceptical kind of person you’ll need more pictures:

This is tetraphenylporphyrin’s emission by excitation with the same laser. The image on the right is just a crop. Here it’s clear that the light is focused somewhere inside the sample liquid.

The A is for asynchronous

In SPI two or more devices communicate and the transmission rate is dictated by the master’s SCLK. Because the SCLK is shared between all devices it’s reliable even at very high speed – the STM32F401RE’s fastest SPI peripheral is good up to 42 MHz.

In UART two devices communicate with agreed-upon speed, character length, parity bit and number of stop bits. To transmit a byte one typically needs to send 10 bits: 1 start bit, 8 data bits and one stop bit. The two devices don’t share a clock – this is the asynchronous part – so if the actual speed of your two UARTs are not the same, you’ll run into trouble at high baud-rates, and that’s exactly what I did.

The remainder of this post is about the exploration of some of the Nucleo board’s various clocks. To spare you from high expectations, the conclusion is that I’ve not reached a higher baud-rate than 230.4 kBps for USART.

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More glass – or less

This isn’t the first post about focus. In the previous post focus it became very clear – to me at least – how important proper focus is for the throughput of the optical system. The previous post was only about the planoconvex lens and the optical fiber. This will be about the microscope objective and the sample.

In the very beginning of my Raman shopping spree I aquired something that looks a lot like a Nikon CFI Plan Apo VC 20X. And you know what they say: If it quacks like a duck..

The microscope objective is very suitable for (this) Raman application because of the very large numerical aperture┬╣ (0.75) and the large diameter of the exit pupil (app. 14mm):

The catch is that the working distance is 1 mm. It’s on the low side of what you’d expect for 20x microscope objective, but I guess it’s the trade-off for the high NA. So what’s the problem with that then?

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A page just for the TCD1304

Even if I’ve not published a lot this year, this blog has become bigger than I ever thought it would be, so much so, that even I have a difficult time finding whatever information I know is here somewhere.

I’ll keep posting here, but I will also create sister-pages (they’ll be here on wordpress.com, but they won’t exactly be blogs) where the information is presented in a more organised fashion.

So I present: http://tcd1304.wordpress.com

You guessed it. It’s all about the tcd1304 and how to play with it.

More better organised pages to follow ..once I figure out what is worth organizing.

Firmware revision

Summer brought a revision of the STM32F401RE TCD1304 driver.

In the firmware for the nucleo board the data collected by the ADC is stored in memory using DMA. Until now the ADC+DMA was turned on by an interrupt created by the timer controlling the ICG-pulses (remember that the ICG pulse moves the pixels to the shift registers on the TCD1304). The ADC and DMA are turned off again by an interrupt created by the DMA-controller once the write-buffer is full.

Enabling the DMA from a timer interrupt is painless, but disabling it using an interrupt triggered by the same DMA-stream that you want to turn off is not. The reason is that disabling the DMA-stream creates a new interrupt – the same interrupt in fact – so you can easily get stuck in the interrupt routine.

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