# Hippocampal Neurons' Alignment on Quartz Grooves and Parylene Cues on Quartz Substrate
## 1 Introduction  
Cell alignment is an important property of certain cell types. Some tissues, such as muscle or nerve tissue, are formed from precisely aligned cells, which are important for proper function of the tissue. Cell alignment in vivo is induced by a complex combination of factors, but cell alignment can be also induced artificially in vivo and in vitro. For in vitro applications, some aligned cells can have different properties in morphology, proliferation, gene expressions, adhesion, and others compared to unaligned cells. Cell alignment and related cell patterning have found application in tissue engineering and regenerative medicine. Methods for cell alignment are often the same or close to methods for cell patterning. Cell alignment in vitro can be induced by various factors [1; 2; 3]; mostly, it is according to the topography of structures on which cells adhere and according to the patterns on the surface created by chemical treatment to which cells have different adhesion affinity. Both these methods are prepared using microfabrication techniques. Less common methods used for cell alignment are electrical stimulation and mechanical loading [4].  
This work is focused on neurons' alignment. Neurons' alignment and patterning is inspired by biological conditions in which neurons grow. During the development of thenervous system, neurons' migration is led, in addition to other factors, by scaffold tracts formed from glia cells. There are numbers of described examples where neurons migrate according to glia scaffolds [5; 6; 7; 8; 9; 10], or where glia scaffolds participate in the regeneration of damaged neurons [11].  
For in vitro alignment, anisotropic structures such as grooves, ridges, and cues are used. Structures for neurons' alignment were tested in different dimensions, materials, and for different cultivation conditions [12; 13; 14]. In these studies, the neurons grew according to the direction of anisotropic structures, but in other studies, neurons' response to isotropic structures was more complex. Neurons from the central nervous system cultivated on grooves have been oriented in both longitudinal and perpendicular direction to the direction of grooves; however, neurons from the peripheral nervous system have always been oriented in perpendicular direction [15; 16]. In another study, neurons were aligned in longitudinal direction on grooves 2 \(\upmu\)m wide and wider; however, neurons were aligned in perpendicular direction on grooves 1 \(\upmu\)m wide [17]. These studies show that neurons are actively sensing their surroundings.  
Selective chemical surface treatment is another effective method for neurons' alignment and patterning. A well-known method is microprinting, where a coating agent is selectively printed on a surface by elevated features from a polydimethylsiloxane (PDMS) stamp [18; 19], and thus, the neurons will adhere only to the coated surface. Among other methods for chemical surface patterning [20; 21], cells can also be patterned by parylene structures on glass substrate [22].  
This work is focused on the difference between neurons' alignment on structures for topographical patterning and chemical patterning. Both these approaches are effective for cell alignment. Structures for topographical patterning are in the form of grooves in quartz substrate and structures for chemical patterning are in the form of parylene cues on quartz substrate.