Three-dimensional imaging of the mucosa of the lower lip and labial minor salivary glands is usually demonstrated using swept source optical coherence tomography (OCT) system at 1310 nm with altered interface. . Implementation of Fourier detection in OCT considerably increased its ability to detect very low signals coming from the imaged objects [24-26]. OCT with wavelength-tunable lasers Fosaprepitant dimeglumine known as swept source OCT (SS-OCT) offers superior overall performance over other detection approaches because of the lower transmission drop with depth better photon detection efficiency and possibility to use dual balance detection plan [27 28 The advantage of OCT over other optical imaging methods such as confocal microscopy stems from the fact that OCT uses coherence gating thus enabling acquisition of three-dimensional (3-D) data in a simple scanning session. On the other hand a stack of images acquired from multiple depths must be used to perform 3-D morphology reconstruction in confocal microscopy. Consequently scanning the tissue multiple occasions is required. Currently OCT is usually widely utilized in ophthalmology where it became standard Fosaprepitant dimeglumine imaging technique used in diagnosis of several disorders of the retina and the anterior segment of the eye . That initial application of OCT was supported by the fact that the eye ERK is composed of transparent structures so that it is usually relatively easy to deliver the light as well as to detect backscattered / backreflected photons. However OCT was also used as a visualization tool Fosaprepitant dimeglumine of other less transparent tissues thanks to the integration of OCT with standard devices like catheters endoscopes laparoscopes laryngoscopes and colposcopes [29-31]. Although majority of those OCT devices run at 1.3 μm wavelengths to enable deeper light penetration most applications involve imaging of subsurface tissue morphology of different organs in human body. In clinical research special attention has been paid to mucous membranes in various parts of the body since many pathological conditions appear as structural and functional abnormalities in the mucosa. Glandular structures were visualized in the skin as well as in the mucosa of e.g. the esophagus colon larynx buccal pouch trachea cervix and bladder [29 32 Initial studies showed that OCT can be helpful in high-resolution imaging of the soft tissues in the oral cavity . OCT imaging was also used to characterize the oral mucosa microstructures in pre-cancerous abnormalities as well as Fosaprepitant dimeglumine in oral cancers [38-40]. Furthermore SS-OCT with hand-held probe was exhibited for labial gland imaging and blood flow in human lips was also visualized with Doppler OCT [41 42 However no quantitative analysis of human lips glandular structures based on OCT data has been performed yet either for the healthy subjects or diseased conditions. The diversity of clinical presentations of Sj?gren’s syndrome has led to development of units of criteria for diagnosis of the disease. In contrast to American-European Consensus Criteria on which this study is based  recently proposed criteria focus more on labial minor salivary gland (LMSG) biopsy by listing it as one of three objective features of Sj?gren’s syndrome . This switch highlights the confirmed diagnostic value of LMSG investigation. Although other modalities for LMSG and major salivary gland analysis exist  so far the specificity of LMSG biopsy remained unequaled [7 45 However the biopsy is an invasive procedure Fosaprepitant dimeglumine that leads to acute and medium term complications in about 10% of patients . Therefore a new non-invasive technique of LMSG examination that would bring benefits comparable to that of biopsy is needed. The aim of this study was to develop a SS-OCT instrument for imaging the mucosa of the lower lip and the labial minor salivary glands along with elaboration of the imaging approach easily applicable in a clinical setting. Another goal of our study was to expose quantitative descriptors of the morphology of LMSGs and to perform comprehensive morphometry of LMSGs in Sj?gren’s syndrome patients and in subjects from a control group. 2 Methods 2.1 Swept Source OCT instrument for imaging oral mucosa and labial minor salivary glands A schematic diagram of the SS-OCT system for imaging the mucosa of the lower lip Fosaprepitant dimeglumine and LMSGs is demonstrated in Fig. 1 . The instrument.