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The Base
The base holds 36 light emitting diodes (LED) as well as the power supply required to drive the LED. The LED are arranged in six rows of 6 LED each. Two rows of red LED, two rows of blue LED and one row each of green and white LED. The reason for the reduced number of green LED is their better brightness performance.

Red Rows: 12 Kingbright L53SRC/F (3.5cd ea, 30dgr, 5mm dia)
Green Row: 6 Nichia NSPG500S (9 cd ea, 15dgr, 5mm dia)
Blue Rows: 12 Nichia NSPB500S (3.5cd ea, 20dgr, 3mm dia)
White Row: 6 Nichia NSPW500BS (6.4cd ea, 20dgr, 5mm dia)

Detailed specs of each LED can be found here. I used Nichia high brightness LED as they currently offer the highest brightness in a 5mm package. Each row (or both rows together in the case of the blur and red LED) is current-controlled by a variable resistor to allow for modulation of the brightness of the row from off linearly to full brightness. The base plate also includes the power supply to support all clusters. For the supply I used a PC power supply from an old computer. The 5V line of such a supply works very well for an LED cluster like this (the LED need between 2.2V to 3.8V depending on the colour).

Each row of LED is connected in parallel and a single appropriate resistor drops the voltage to the requirement of the LED followed by the variable resistor that controls the brightness of each row. You can find the circuit board layout here.
I build a simple metal box and added it to the side of the power supply. A 5cm x 5cm square hole on the top of the extra box allows the LED cluster to send light into the lightpipe which is mounted on top of the box. To diffuse the light coming from the LED cluster I covered the hole with a Lexan 30 degree diffuser but this isn’t essential if you cannot obtain a good diffuser.
Around the hole in the base cover I put 4 Rare-Earth Super Magnets available at RadioShack as mounting points for the filter lightpipe. The 4 control knobs (i.e. the variable resistor knobs) are mounted on the side of the box.