A programmable LED device that illuminates multiple spatial locations (termed wells) with user-defined light patterns whose intensity can be modulated as a function of space and time. The devices are used for optogenetic stimulation of tissue culture plates (24-well and 96-well) kept in a heated and humidified tissue culture incubator, as well as photopatterning of hydrogels. In brief, light from LEDs passes through optical elements that ensure uniform illumination of each well. Parameters of the optical system, such as LED configuration, optical diffuser elements, materials, and geometry, were modeled and optimized using the optical ray tracing software Zemax OpticStudio. An electronics subsystem allows programmed control of illumination intensity and temporal sequences, with independent control of each well. Spatial precision is conveyed through a photomask attached to the culture plate. The hardware design also includes a cooling system and vibration isolation to reduce heating and damage to the sample. Lastly, a graphical user interface (GUI) was used to wirelessly program the illumination intensity and temporal sequences for each well. The devices can thus illuminate 24 independent channels with visible, NIR, or UV light with intensity ranges of 0 to 20-100 microwatts per millimeter-squared with 16-bit intensity resolution, and a temporal resolution of 1 millisecond and spatial resolution of 100 microns. In summary, the device allows uniform illumination of multiple wells for multiplexed photoactivation or photopolymerization of various substrates (light-responsive bacterial or mammalian cells grown in tissue culture, hydrogels, dyes, etc) with user-defined patterns. The device can be combined with a robotic handler, microscope, spectrometer, etc, to enable high-throughput illumination and simultaneous recording of the sample.