Monthly Archives: July 2015

Using near IR to look for photosynthesis and plant health with NDVI

The NoIR Raspberry Pi camera comes with a blue filter to do near infrared photography – the blue filter ices the visible red but passes near IR which records as red, apparently.

NDVI image of something in the polytunnels

NDVI image of something in the polytunnels. Should have made a not of what this plant is 😉 Anyway, more red and going to magenta white overload=more photosynthesis

NDVI (Normalized Difference Vegetation Index) is the near IR plus red divided by near IR minus red. Take a look at this image for the meaning of the colours – red, magenta and white is more photosynthesis, cool colours and black are less. Chlorophyll uses red but doesn’t use near IR which it reflects, hence the difference carries useful information.Lots more at Public Lab. Continue reading

Measuring paramagnetism 2 – a new sensor

Part 1

Since I will be taking the sensor to the rock I’m going to temporarily give up on getting an absolute measurement, and take a leaf out of Bartington’s book from last time and use a flat coil. I will never be able to contain the sample in the magnetic field 1 as I might be able to in a solenoid, to the effective susceptibility will always be lower than 1. One day I may be able to calibrate this and find a fixing factor, but for now I will look for relative differences.

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Notes:

  1. unless I grind a slot in the rockface and put the coil into it I suppose 🙂

Measuring paramagnetism

There are two approaches to measuring paramagnetism that seem to be common. One is to use a balance to measure the slight attraction to a magnet – put sample in a balance, apply magnetic field, look for difference in weight of sample using a Gouy balance or use a torsion balance to observe the attraction in a horizontal plane which takes out the static weight of the sample.

The trouble with these two is the attraction due to paramagnetism is weak compared to the weight of the sample – these are lab bench instruments and the electromagnet consumes a lot of power. Although taking samples of soil is easy enough to bring back to the lab, one really shouldn’t be taking a hammer and chisel to ancient monuments to get a sample for a Gouy balance 😉

It's not really right to go chiselling a lump off this to insert into a Gouy balance...

It’s not really right to go chiselling a lump off megaliths that have survived thousands of years to insert into a Gouy balance…

The other way of measuring volume magnetic susceptibility is to stick the sample into a coil and measure the inductance – with a different configuration  of the coil as a search coil it can be used to measure susceptibility at the rockface.

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Paramagnetic soil ponderings and perambulations

Paramagnetism is a reasonably straightforward characteristic of materials – if there are unpaired electrons in the atoms then the element will be paramagnetic and weakly drawn to a magnet. This demo of oxygen being paramagnetic is great – so far so scientific. Compounds can change this – water is diamagnetic although H2O is clearly contains oxygen.

A lump of paramegnetic rock (the coin is ~2cm dia)

A lump of paramagnetic rock (the coin is ~2cm dia)

When applied to soil and the growth of plants, however, paramagnetic effects fall into the domain of the woo-woo rather than the analytic 🙂 Igneous rock and volcanic soils tend to be notably paramagnetic. Philip Callahan is the go-to source, and this extract from a 1995 Acres USA article is a high-level spin on his take : Continue reading

Using the microscope to grade compost and compost extract

This is using Elaine Ingham’s microscopy techniques to investigate thermal compost – some of what I saw. I am at an early stage of being able to do this, so any errors are mine and not Elaine Ingham’s 😉 The principle is to classify organisms by their morphology – aerobic fungi tend to have a colour, diameter wider than 2.5µm and/or have uniform septa. Spiral structures are bad, indiciative of anaerobic conditions, and ciliates (hairs all over the body) also indicate anaerobic – bad- conditions. Apart form the spirochete most of these are good.

This is on a 5x dilution, the recommended intial conditions (use 1ml of compost and make up to 5ml total with water left to stand so the chlorine has gone).

Weatherizing a Raspberry Pi Camera with a Microscope slide

Sticking a Raspberry Pi camera exposed to the elements doesn’t do it any good over time, resulting in the hazy crazed lens problem.

Flare on the camera lens after a year in the open

Flare on the camera lens after a year in the open

The solution is to put some glass in front of the lens – and indeed this is exactly what this commercial outdoor spec little lipstick CCTV camera does

it's hard to see, but there is a round glass against an O ring in gront of the camera lens on this weatherpoof camera, which has spent several years outside and still works well

it’s hard to see, but there is a round glass against an O ring in gront of the camera lens on this weatherproof camera, which has spent several years outside and still works well

I discovered this when I took it apart to unscrew the lens a bit to make a close focus. And then cracked the glass refitting it as the lens stuck out too much. If you ever need a flat round piece of glass, search for watch crystal on ebay and they are to be had in lots of diameters. A watch crystal is apparently a term for the glass on a watch as well as the 32,768 Hz timing quartz crystal. A flat watch crystal repaired this camera.

The direct exposure of the camera lens to the elements is the biggest weakness of the now-defunct PICE weatherproof Pi case. But it is easily rectified now, using a piece of flat glass fitted with Sugru or Milliput putty. I used sugru and a cut down microscope slide, since I didn’t want to buy another watch crystal when microscope slides are optically flat and cheaper. It is a lot easier to cut glass under water, and you can remove the viciously sharp edges using a cheap diamond sharpening stone to smooth the cut edge and chamfer the corner.

Microscope slide fitted with Sugru to shed the water and seal the camera from the elements

Microscope slide fitted with Sugru to shed the water and seal the camera from the elements

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Making Compost Extract

The easiest and low-tech way of adding the microorganisms from compost is to extract them fro mthe compost using water and a mesh, then spray the water  – in our case using watering cans. You can spread the compost itself, and there’s much to be said for that, but it’s more stuff to wrangle and needs to happen before you plant, ideally. Since we are going to test areas on already growing plants, extract it is. Compost tea is a way of getting more microbes out there, but it is technically harder and we don’t have the gear. Extract it is, then. The rate seems to be about a good handful per 5 gallons, we used half an IBC, ie about 500 liters, which is 110 gallons. So we need about 20 times as much

Start with a wodge of compost in a net curtain

Start with a wodge of compost in a net curtain

and some reasonably clean borehole water (so no worries on chlorine or chloramine)

and 500 litres reasonably clean borehole water (so no worries on chlorine or chloramine)

We made a bag by putting the compost in the middle of the net curtain material and tying up the top with a releasable cable tie.

You can see the brown of the humic acid leaching out of the compost into the water

You can see the brown of the humic acid leaching out of the compost into the water

the end result is a dark brown chocolate colour

the end result is a dark brown chocolate colour

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