In one aspect, the disclosure provides a method of defining a Raman signature of a culture component, the method comprising: obtaining a Raman spectrum of a culture component in a non-interfering or minimally-interfering solution, identifying peaks in the Raman spectrum that are associated with the culture component, obtaining a Raman spectrum of a culture medium comprising the culture component, and, removing peaks of the culture component in the Raman spectrum of the culture medium that are distorted compared to the peaks identified in the Raman spectrum of the culture component in a non-interfering or minimally-interfering solution.

Various embodiments provide systems, methods, and apparatuses for detecting optical fluid detection. The apparatus may include an optical source configured to emit one or more optical test beams. The apparatus may further include a first mirror configured to reflect the one or more optical test beams. The apparatus may further include a plurality of fluid cells including a first fluid cell configured to pass the one or more optical test beams through a first fluid. The apparatus may further include a second mirror configured to reflect the one or more optical test beams after passing through the first fluid cell. The apparatus may further include a third mirror configured to reflect the one or more optical test beams after reflecting from the second mirror. The apparatus may further include an optical detector configured to receive the one or more optical test beams after reflecting from the third mirror.

The inventions provide microscopes for imaging samples within wells of multi-well plates. Microscopes of the disclosure include a beam homogenizer system that shapes a beam from a light source into a shape specific to the bottom of a well of a multi-well plate. In particular, microscopes of the disclosure can illuminate wells for imaging by passing light through a prism that is beneath the sample. The light enters the prism from the side and as refracted into the well at a steep angle such that the light only illuminates about a bottom ten microns of the well. The beam homogenizer shapes the light from the light source so that, instead of hitting the prism as a spot with an irregular shape, the light enters the prism in a substantially rectangular pattern with homogeneous optical power level over the pattern.

Provided herein is a stimulation and measurement device. The stimulation and measurement device includes a microwell plate having a top side, a bottom side, and at least one well extending from the top side towards the bottom side; a first assembly removably positioned on the top side of the microwell plate; a second assembly removably positioned on the bottom side of the microwell plate; and a microcontroller. The first assembly includes a first printed circuit board having at least one pair of stimulating light emitting diodes (LEDs) positioned thereon to align with one of the wells. The second assembly includes a second printed circuit board having at least one photodiode positioned thereon to align with one of the pairs of stimulating LEDs, and at least one excitation LED paired with each of the photodiodes. The microcontroller is configured to control the stimulating LED(s), the photodiode(s), and the excitation LED(s).

Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An apparatus can include an assay chip that includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits emission energy; at least one element for directing the emission energy in a particular direction; and a light path along which the emission energy travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the assay chip. The instrument includes an excitation light source for exciting the sample in each sample well; a plurality of sensors corresponding the sample wells. Each sensor may detect emission energy from a sample in a respective sample well. The instrument includes at least one optical element that directs the emission energy from each sample well towards a respective sensor of the plurality of sensors.

The inventions provide microscopes for imaging samples within wells of multi-well plates. Microscopes of the disclosure include a beam homogenizer system that shapes a beam from a light source into a shape specific to the bottom of a well of a multi-well plate. In particular, microscopes of the disclosure can illuminate wells for imaging by passing light through a prism that is beneath the sample. The light enters the prism from the side and as refracted into the well at a steep angle such that the light only illuminates about a bottom ten microns of the well. The beam homogenizer shapes the light from the light source so that, instead of hitting the prism as a spot with an irregular shape, the light enters the prism in a substantially rectangular pattern with homogeneous optical power level over the pattern.

Provided herein is a stimulation and measurement device. The stimulation and measurement device includes a microwell plate having a top side, a bottom side, and at least one well extending from the top side towards the bottom side; a first assembly removably positioned on the top side of the microwell plate; a second assembly removably positioned on the bottom side of the microwell plate; and a microcontroller. The first assembly includes a first printed circuit board having at least one pair of stimulating light emitting diodes (LEDs) positioned thereon to align with one of the wells. The second assembly includes a second printed circuit board having at least one photodiode positioned thereon to align with one of the pairs of stimulating LEDs, and at least one excitation LED paired with each of the photodiodes. The microcontroller is configured to control the stimulating LED(s), the photodiode(s), and the excitation LED(s).