How to control multiple tiny PWM controllers with one "master" MCU; DIY LED array
There are dimmer controllers made specifically for LEDs.  Have a look at PCA9532 and PCA9536 for an example.  These are controlled through I2C bus.  They have 3 address bits, which allows to control 8 of them with one I2C bus.  

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You need to write down more fundamental aspects of your experimental setup such as: desired light output, wavelengths, models of LEDs, number of LEDs, should you use PWM or linear control.  Digital control is nice and convenient, but I wouldn't be too concerned about that at an early stage of the experiment design that you are currently at.