Introduction

Rome, known as Aeterna Urbs (the Eternal City), is a place that combines modernity with relics of past eras. Although many archaeological traces are lost or buried beneath two and a half millennia of subsequent urban growth, new artefacts have been brought to light thanks to successive scientific research. Recent deep excavations and the increasing use of environmental methodologies are starting to change our understanding of the urbanisation process in Rome. Some ancient basilicas have witnessed a rich and changing history, so their analysis can provide valuable insights into the development of construction techniques and architectural styles. Rome is an exceptional illustration of 2700 years of architectural heritage and urban artistic solutions integrated within a single urban environment1.

The significant challenges in preserving historical heritage spanning several centuries include the lack of systematic knowledge about the architectural and structural changes that have occurred in a particular facility. It is often the case that both technical documentation and historical records of changes are lacking. A detailed examination of the space, including room heights and the arrangement of paintings, is conducted to comprehend the causes and characteristics of changes. Through the identification of spatial and geometric parameters, it is possible to hypothesise regarding the prior functional uses and delineate the various developmental phases of the structure. Photogrammetry has long been utilised as a method for gathering three-dimensional (3D) data of cultural heritage2,3. Multispectral cameras and 3D scanners gather complementary data-spectral and spatial-facilitating the archiving and visualisation of inheritance4. Additionally, 3D reconstruction involves capturing and reproducing the shape and characteristics of any object or scene using depth and colour data5. Aside from photogrammetry, which is understood as the art and science of determining the position and shape of objects from photographs, computer vision can also be applied. This mathematical technique involves recovering the three-dimensional shape and appearance of objects in imagery6. The spatial understanding of a heritage site through photogrammetry can be expanded with other methods, such as 3D high-resolution ground penetrating radar (GPR)7, infra-red thermography (IRT), microwave reflectometry (MWR) and digital holographic speckle pattern interferometry (DHSPI)8. The collection of various data can be fundamental for creating a BIM model and developing a framework for restoration9.

This article presents a comprehensive study comprising two phases. In the first phase, a thorough systematic review of the current state of knowledge was conducted regarding the successive architectural changes in the Basilica of Saint Chrysogonus (it.: San Crisogono). In the second phase, the research employed an integrated survey that utilises two-dimensional models to facilitate the evaluation of historical-interpretive hypotheses. This study seeks to combine metric-geometric features essential for managing spatial relationships among the paintings. These features enable the reconstruction of the spatial layout, ceiling heights, and usage of the spaces. To overcome the challenges of scanning such a complex space, a structure from motion (SfM) approach was implemented10,11. Based on the obtained results, a contour analysis was conducted, and a digital elevation model was developed. In light of the site’s complexity, it is crucial to contextualise the basilica not only through its architectural evolution but also within its broader urban and geographical setting, which are integral to understanding its historical development and current cultural significance.

St. Chrysogonus Basilica is in the heart of one of Rome’s oldest districts—Trastevere, on the west bank of the Tiber River. Today, Trastevere stretches between the western bank of the Tiber River, the Prati district to the north, Monteverde to the south, and Aurelio to the east. Trastevere, being the most isolated section of Rome, had the opportunity to develop a distinct character12. For this reason, the buildings in this part of the city should constitute valuable historical evidence. The contemporary basilica of Saint Chrysogonus is located near the Tiber River, approximately 150 metres south of Garibaldi Bridge (Fig. 1). The main eastern façade is on the square Piazza Sidney Sonnino—Fig. 2, and the northern façade adjoins Largo S. Giovanni de Matha.

Fig. 1: Location of the Trastevere district and the Basilica of St. Chrysogonus in Rome.
figure 1

a) Map of the entire city of Rome, with the Trastevere district highlighted in red; b) Map of the Trastevere district, with the location of the Basilica of St.Chrysogonus highlighted in purple; c) Enlarged view of the area surrounding the Basilica.

Fig. 2: The eastern façade of Basilica of St.
figure 2

Chrysogonus: a bell tower, b baroque entrance.

Methods

The methodological framework adopted in this study comprises two complementary components: a historical-literature review aimed at reconstructing the architectural evolution of the Basilica of Saint Chrysogonus, and a spatial-metric analysis supported by photogrammetric surveying techniques (Fig. 3). The first phase of the research involved a detailed review of historical and scholarly sources to identify and analyse successive architectural transformations of the basilica. This included written historical plans, archaeological reports, and previous conservation studies. The objective was to reconstruct the chronological sequence of structural modifications and to contextualise them within broader historical and urban dynamics. The outcomes of the historical review shaped the interpretative framework for the spatial analysis. In particular, hypotheses concerning the original spatial organisation and successive alterations were tested and refined through metric data obtained from photogrammetric scanning.

Fig. 3: Research methods used in this study
figure 3

Schematic diagram illustrating the step-by-step approach, including historical and scientific data review, digital data acquisition, and cross analysisprocedures.

Today, the lower Basilica of Saint Chrysogonus is significantly compromised due to the challenges of interpreting its unique spatial configuration. Accessible through the upper basilica of the same name, this Early Christian structure appears as a palimpsest—both artistically, due to the stratification of distinct stylistic and chronological painting sequences on the same wall surfaces13, and archaeologically and architecturally, because of the intense intermingling of original structures, later interventions, restorations, and structural reinforcements. This complexity necessitates a systematic analytical approach, capable of defining the terms of the problem by moving from the known (existing traces) to the unknown (reconstructing the past).

The survey campaign provided an opportunity to once again test the effectiveness of integrated methodologies, now well-established in specialised scientific fields, on a complex architectural structure that combines the tangible volumetric and spatial presence of seventeenth-century architecture with the often barely perceptible traces of the Early Christian basilica’s archaeology. In this sense, integration is no longer understood merely as the synchronous and coordinated use of different survey methods but increasingly as the convergence of multiple disciplines that, through data sharing, contribute to a deeper understanding of the studied object.

Easily manageable and comprehensible two-dimensional and three-dimensional models were developed, with particular attention given to the spatial positioning of pictorial elements. Existing surveys lacked a unified and unequivocal framework that could map the wall paintings, now found in separate spaces but originally part of a continuous spatial entity. The possibility of synchronously analysing different pictorial elements using two-dimensional models enabled the evaluation of historical-interpretative hypotheses and was a key reason for conducting an integrated survey. Thanks to the final digital models, a contextual reading of both the morphology of the Early Christian church—often preserved only in wall remnants within a complex mix of collapses and alterations—and its decorative elements was made possible, thus enabling specialised studies of the site.

The assessment of methods and techniques employed in the integrated survey stemmed directly from identifying specific knowledge objectives related to the structure. During the investigations within the Early Christian basilica of Saint Chrysogonus, it was necessary to acquire 3D data within a limited timeframe, in compliance with site protection and safety requirements. For the lower basilica of San Chrysogonus, the 3D integrated survey encompassed the apse, the baptistery, accessible portions of the hall, and traces of the narthex on the eastern side, along the entrance, as well as adjacent spaces that attest to different construction phases. Beyond the lower basilica itself, the survey campaign extended to the passage, connecting it with the upper basilica and a portion of the latter, allowing for an evaluation of the spatial relationship and axial alignment between the two structures.

All the areas were surveyed, integrating 3D laser scanner data capturing with photogrammetric processes. The 3D laser scanner (Faro Focus CAM2 M70) acquisition aimed to provide dimensional and morphological data at the architectural scale. A total of 76 scans were captured and then aligned together based on a cloud-to-cloud alignment algorithm. The scan’s position was designed to ensure proper overlapping, with an average of 50% for each couple of scans, and to minimise the unsurveyed areas. Additionally, the scan path was designed to ensure close paths, aiming at maximising metric accuracy. All the scans included RGB data captured thanks to the integrated camera of the 3D scanner.

The nature of the investigation context determined the survey methodology to be adopted: the limited accessibility of the wall frescoes and the peculiar spatial configuration of the underground basilica made it essential to implement SfM (structure from motion) acquisition systems. These methods ensured complete coverage of the area while producing a virtual model that is both easily interpretable and metrically reliable. In this context, it was decided to employ SfM processes using UAVs (unmanned aerial vehicles)14, not only for their cost-effectiveness and portability but also to overcome the limitations imposed by the static nature of laser scanner acquisition setups. For the lower basilica, approximately 850 images were captured using a DJI Mavic AIR PRO, uniformly distributed across the accessible portions of the hall, the narthex, the apse, and the baptistery. Particular attention was given to recording the fresco fragments located in the upper sections of the walls. Given the complex spatial morphology, the use of a UAV system for image capture maximised survey coverage by accessing areas that would have otherwise been unreachable. The archaeological area of the Lower Basilica comprises relatively wide spaces that are well-suited for UAV-based survey operations. Simultaneously, certain areas present accessibility challenges for terrestrial laser scanning, but can be effectively documented using UAV systems. UAV photogrammetry was complemented with handheld camera captures (using Nikon D800 with Nikkor 28 mm and 50 mm lenses) to ensure higher resolution and greater detail, particularly for the frescoes. Concerning the image acquisition of the frescoes, the distance between the camera and the surfaces was limited because of the spatial articulation. This condition influenced the data capturing strategies in terms of how to illuminate the frescoes properly. The primary objective was to ensure high radiometric fidelity in the resulting orthoimages. To this end, during handheld camera data acquisition, the scene was illuminated using LED lights with a known colour temperature, strategically positioned to provide uniform lighting across the surfaces. This setup ensured accurate colour reproduction and facilitated post-processing operations, particularly in terms of white balance correction.

The 3D model generation process was conducted semi-automatically, beginning with photographic acquisition. Thanks to the photogrammetric workflow, all images acquired via handheld cameras and UAVs were then processed using Agisoft Metashape software to generate a 3D point cloud. This point cloud was subsequently scaled and refined through a bundle adjustment, utilising the 3D coordinates of homologous points, used as control points, that were clearly identifiable in both the laser scanner and photogrammetric point clouds. A total of 27 homologous points were detected in both point clouds and were used for the scaling process directly in Agisoft Metashape software. The 27 homologous points were uniformly detected on all the surfaces to guarantee a homogeneous distribution of the metric error. This procedure enabled the evaluation and verification of the metric and geometric accuracy of the SfM-derived point cloud, resulting in a total error of 1.2 cm, as well as its alignment with the laser scanner dataset. Moreover, the two models were integrated to combine the morphological and dimensional precision of the laser scanner data with the radiometric detail provided by photogrammetry. The integrated point cloud was used as a basis for 2D representations at 1:50, to elaborate 2D high-resolution ortho-images and for the 3D modelling and reconstruction.

Beyond a purely stylistic analysis of the surviving painted fragments, the study aims to integrate their metric-geometric characteristics, necessary for controlling spatial relationships between the paintings, with their figurative aspects, which help reconstruct the original composition of each scene. This approach supports hypotheses regarding the spatial configuration, room heights, and the use of these spaces. This symbiotic relationship between architecture and painting demands a holistic approach, where pictorial traces inform architectural interpretation, and conversely, architectural traces provide the necessary context for analysing the paintings.

Results

Historical artefact

St. Chrysogonus Basilica is a parish and titular church, meaning the Pope assigns this temple to a cardinal. The church also ranks as a minor basilica, given to churches distinguished by their historical, liturgical, and pilgrimage value. It is also a station church from the fifth Monday of Lent15. The church is dedicated to Saint Chrysogonus. His figure is confirmed in late antique hagiographic texts, such as the Passio Anastasiae and the Passio Cantianorum. According to legend, Saint Chrysogonus was an educated and influential Roman citizen of high social standing. Saint was to be executed during the persecution of Christians during the reign of Emperor Diocletian (c. 303 AD). According to tradition, he was beheaded at a place called Ad Aquas Gradatas, near Aquileia. Later, according to Zadar legends, his relics were to be transferred to Zadar, where he became the patron of the city. Historians agree that St. Chrysogonus is a historical figure, although many details about his life and death are derived from hagiographic legends. Early evidence of his cult in Aquileia, Milan, Ravenna and Rome indicates his real presence in the Christian tradition16. One of the mentioned traces of the cult is the basilica of Saint Chrysogonus in Roman Trastevere. The church may be divided into two principal sections: the lower and the upper. The lower section comprises an underground Early Christian basilica, likely dating back to the 5th century. The upper section includes a medieval basilica constructed in the 12th century, although it presently exhibits Baroque characteristics introduced in the 17th century17,18. Frequently, Early Christian churches bear the cumulative effects of successive alterations, particularly evident in their external architecture. These structures, enhanced with Romanesque towers, embellished with Renaissance porticos, and subsequently adorned with Baroque façades, provide a testament to the evolution of architectural styles spanning the medieval period to modernity19. Over time, the basilica experienced stylistic changes and shifts in its occupants20—Table 1.

Table. 1 Changes in the guardians of the Basilica of St. Chrysogonus in Rome over the centuries

Early Christian Basilica

Although the early Christian monument has been known for a long time, active research work began in 190721. The Trinitarian Fathers noticed a round wall in their sacristy’s basement, which was the reason to start the work. Marucchi performed the first research (apse, annexes and chancel). The second investigation stage was in 1914 when the southern part of the basilica was discovered. Almost ten years later, Mancini explored the northern part more thoroughly21,22. There is no difficulty in identifying the church building. There is a file of reliable, albeit late, texts. The first dates back to 499: three priests, who claimed to be of the titulus Chrysogoni, signed the acts of a council. The evolution of the titular designation is intriguing: in the year 499, it was referred to as Chrysogonus, which subsequently transformed into Sanctus Chrysogonus in 521. In the first case, the title evokes a founder; in the second, it refers to the saint of Aquileia. In the early 6th century, the calendar from Carthage designates 24th November as the feast of a martyr—a saint from Aquileia—rather than the anniversary of its Roman founder. This detail could support the identification of the saint as St Chrysogonus of Aquileia21.

The lower basilica is accessible via a staircase in the sacristy of the upper basilica. Sources propose the possibility of constructing a new basilica following the demolition of the old structure23; however, research indicates that the original building has endured to this day. The dating of the lower basilica of Saint Chrysogonus remains a subject of scholarly debate, with several theories presented. Krautheimer and Apollonj Ghetti suggest dating the structure to either the first or second half of the 5th century13, a proposition consistent with the theory that its construction occurred shortly before its earliest documented reference in 499 AD21. Krautheimer further identifies the lower basilica of St Chrysogonus as potentially originating in the 4th century19.

An alternative theory postulates the presence of an even earlier structure, whose remains were incorporated into the Early Christian basilica. This earlier construction is evidenced by walls in the eastern apse section, dated to the 4th century. Maurice Mesnard proposes a later dating, attributing a height discrepancy of approximately 50 centimetres between the flooring of the 4th-century hall and that of the apse to the passage of significant time between their respective constructions. Similarly, Theodora Leonore Heres, through an analysis of wall structures at varying elevations, dated the basilica to the transition between the 4th and 5th centuries13. Nevertheless, this evidence remains inconclusive, as the difference in floor levels may also be plausibly attributed to the existence of now-lost staircases.

Archaeological excavations uncovered an Early Christian basilica situated five metres below the ground level of the Baroque basilica of St Chrysogonus, which was constructed in the 12th century and features Baroque décor dating to the 17th century21,23. The subterranean positioning of the Early Christian basilica may be attributed to ground subsidence caused by flooding from the Tiber River, a phenomenon frequently described by papal biographers and known to have affected Rome before the 8th century17.

The underground basilica spans 35.35 m in length, with an irregular width ranging from 17.25 m in the east to 19.65 m in the west. At the eastern end lies a narthex (vestibule) measuring 7.25 m in width, while the western end concludes with an apse 10 m wide and 7.40 m deep. On the northern side are rooms of uncertain function, whose inner wall likely aligns with the southern wall of the above-ground basilica. To the south, a baptistery is located, identified by the presence of a basin. Within the apse, a height difference of 0.46 m is evident21. The rectangular structure, located initially at the centre of the basilica, is currently obscured by the foundations of the upper basilica and accumulated rubble22.

There are many uncertainties regarding the exact layout, roof structure, and lighting of the church. At the end of the 19th century, a roof tile similar to those dated to the late 5th or early 6th century was discovered, likely relating to the apse’s roofing13. The construction of the current basilica destroyed the western façade. At the same time, work conducted in the 9th century led to the destruction of the eastern wall, the course of which can only be partially reconstructed. The southern wall of the new basilica aligns with the left wall of the right aisle of the lower basilica (Fig. 4), but the wall separating the filled central nave from the aisle is secondary in origin. It is presumed that the structure originally had two entrances on the southern side, whereas three irregularly placed openings on the northern side were added later. The sources analysed suggest a hypothesis that the building functioned as a domus ecclesiae; however, there is insufficient evidence to support this claim, and some literature indicates that this is unlikely21.

Fig. 4: Layout of the new basilica in relation to the Paleochristian temple.
figure 4

Diagram based on Mesnard’s findings63, illustrating how the structures from different periods overlap.

On the walls, valuable frescoes have deteriorated over time due to persistent moisture and destructive factors, including salts and fungi. These frescoes date from various periods in the Early Medieval structure24. On the southern wall of the lateral nave, a palimpsest of layers of paintings is visible. Over the years, theories regarding their chronology have changed; however, Anna Melograni has identified two distinct decorative phases. Stratigraphic analysis of samples revealed that the older frescoes were created using the al fresco technique, while the later ones employed the al secco method.

The difference between the two types of plaster is apparent to the eye; the high-quality first plaster contrasts sharply with the lower-quality second, which is rough, with large inclusions and signs of straw13. The al fresco technique (Italian pittura a fresco) involves painting on wet plaster, covered with several layers of mortar and pigments resistant to the alkaline action of lime, applied with rainwater (soft water). On the other hand, the al secco technique (Italian “dry”) involves painting on dry plaster with pigments mixed with water, and the binding medium could be lime milk, casein, glue, oil, resins, wax, or whole egg or egg yolk. It is generally accepted that the fresco technique is more labour-intensive, allowing no room for corrections or changes, but it is one of the most durable forms of wall painting25,26. Historical sources indicate that the al secco technique was commonly used from antiquity up to the 14th/15th centuries25, along with mixed fresco-secco methods (according to the post-Byzantine technique, painting began on damp plaster (al fresco) and was completed by the al secco technique27). However, research reveals possible early beginnings of the al fresco method in preliminary drawings painted while the mortar was still damp in ancient BCE times. The first fresco executed in the Mediterranean area was the wall paintings in the Yarim-Lim Palace in Antakya, Turkey28,29,30. Accurate identification of the technique employed in creating the paintings is crucial for appropriately executing potential restoration interventions31.

Returning to the paintings in the analysed church, thematic analysis and the style of the preserved paintings from the first phase (such as the three Jews saved by an angel in the fiery furnace and the Madonna Enthroned) suggest they were likely created in the early 6th century13. The Early Medieval phase is also characterised by the insertion of a semi-circular crypt in the presbytery, modelled after a crypt built in the late 6th century in the original Basilica of St. Peter in the Vatican17. The later layers probably date to the 8th century, featuring saints in medallions and imitations of drapery, which were improved upon those from the 6th century13.

On the northern wall, paintings from the 8th century and the first half of the 11th century are preserved, arranged in three registers. The two lower registers feature hagiographic scenes, including St. Benedict, St. Sylvester, and St. Panteleimon. The third register features drapery motifs dating to the 8th century—evidence of interventions by Pope Gregory III (pontificate 731–741), as recorded in the Liber Pontificalis13,32. The paintings on the northern wall are surrounded by a painterly architectural imitation— twisting columns and architraves—likely alluding to fresco cycles that adorned Early Christian basilicas, such as those of St. Peter and St. Paul24,32.

The single-nave apse (Fig. 5) was probably executed using the opus sectile technique with marble slabs from a previous 4th-century hall discovered during excavations by Giovacchino Mancini13. Opus sectile refers to a Roman art technique in which materials (commonly stone and glass) were cut and inlaid into walls and floors to form a picture or pattern33. The wall paintings in the annular crypt of the first Saint Chrysogonus date to 731–741—Richard Krautheimer terms them a “second Hellenistic wave,” corresponding to the second decorative phase (8th century)17.

Fig. 5: Apse of the lower Basilica of Saint Chrysogonus.
figure 5

Sketch based on Mesnard’s findings63, showing the apse with its labeled architectural elements.

In the apse, there is an example of a quincunx with circles and an “X” connecting them, which is attributed to the time of Pope Gregory III34. However, the paintings in the apse and the corridor of the crypt are generally dated to shortly after the mid-11th century. The mentioned quincunx motifs later developed into the art form known as Arte Cosmatesque.

To sum up, the Early Christian basilica, partially preserved underground beneath a contemporary structure, likely dates back to the 4th or 5th century, with some evidence suggesting even earlier origins. Its architectural evolution reflects multiple phases of construction, destruction, and restoration, accompanied by rich fresco decorations spanning from the 6th to the 11th centuries. Despite uncertainties regarding some structural details, the basilica remains a significant monument illustrating early Christian art, religious practices, and urban development in Rome.

The Medieval times to Baroque Flair

The basilica visible today on Piazza Sidney Sonnino in Rome (Fig. 6), along with the monastic complex, was constructed between 1116 and 1137 as the titular church of Cardinal John of Crema (died around 1135). Cardinal John sponsored the new complex on the site of the early Christian basilica; by 1123, the monastic quarters with cloisters and a chapel were completed23. According to sources, the new basilica was likely built after the demolition of the old church down to a height of 4 m, with its interior filled with rubble. The medieval structure was probably finished in 1129 as a three-nave basilica with a transept. The transept does not extend beyond the body of the building, and the proportions of the interior (excluding the apse and portico) appear intentional, forming a length-to-width ratio of 2:1 (two squares with sides measuring 23.25 m, close to the Roman unit of 100 cubits)35.

Fig. 6: Layout of the medieval (upper) Basilica of Saint Chrysogonus.
figure 6

The layout based on M. Cigola’s plan40, showing the layout with labeled architectural elements.

The medieval façade (Fig. 7a) features a four-column porphyry portico with Ionic capitals supporting a corniced architrave adorned with a frieze. Flanking the central structure, the architrave is further supported by two pilasters, also with Ionic capitals. The central bay of the colonnade is markedly wider than the lateral bays, which may originally have been enclosed by retaining walls. Above the colonnade, a sloping roof is visible. Notably, the medieval columns were repurposed as spolia during the Baroque renovation (Fig. 7b)35,36, although they no longer conform to the original Ionic order.

Fig. 7: Comparison of the medieval and Baroque façades of the Basilica of Saint Chrysogonus.
figure 7

a The medieval façade, reconstructed based on an illustration by Girolamo Franzini from 1588, as cited in Claussen’s research35; b The current Baroque façade. This comparison illustrates the architectural evolution of the church over time.

The interior features several orders of capitals referencing antiquity. Granite colonnades with Ionic capitals separate the central nave from the aisles. In contrast, massive porphyry columns with Corinthian capitals support the triumphal arch, which divides the transept from the central nave—these are the largest surviving medieval columns in modern Rome. Corinthian pilaster capitals support the beginning and end of the architrave. It is speculated that the antique capitals of the columns may have been spolia (reused materials from earlier structures). The church is well-lit through the clerestory (a series of windows above the architrave), and the architraves create a perspectival connection with the altar23,35,37.

The new church was not constructed directly on the site of the old one but is slightly shifted to the north (Fig. 4). The foundations of the southern (left) perimeter wall are situated just to the right of the old apse. These foundations run parallel to the original church, but not closely enough for the side walls of the old church to have served as a foundation for the new structure35.

The medieval period of the basilica is represented by the main altar, which contains the relics of Saint Chrysogonus, consecrated in 1127 by Cardinal John of Crema. The altar takes the form of a chest resting on a richly profiled base with pilasters at its corners35,38. Slightly higher, in the apse, a mosaic depicts the Virgin Mary with the Child Jesus enthroned between Saint James the Great and Saint Chrysogonus. This work is attributed to the school of Pietro Cavallini (approx. 1240–approx. 1330). It is dated to around 129017,39. In the Church of St. Chrysogonus, as in other medieval churches of Rome, examples of floors in the Arte Cosmatesque style can be found. These are geometric floors crafted by artists known as the Cosmati, using materials such as marble, porphyry, and granite. Nicola Severino extensively discusses such floors in his monograph38. Other notable examples of Cosmatesque floors can be found in churches such as San Clemente, Santa Maria in Cosmedin, San Lorenzo fuori le Mura, San Saba, San Giovanni in Laterano, Santa Maria Maggiore, and Santa Maria in Trastevere (with the latter three having been restored)34,38. In St. Chrysogonus, there is an example of this precious flooring.

The original Cosmatesque floor in this church was likely created between 1123 and 1129, potentially extending into the early 12th century40. It is believed to have undergone restoration between 1180 and 1185 by Lorenzo di Tebaldo. Research by Nicola Severino suggests that the floor has undergone multiple renovations over the centuries, particularly during the 17th and 19th centuries, with an estimated replacement of approximately half of the original marble. Regrettably, the sections reconstructed during various historical periods, particularly within the side aisles, are marked by the substitution of original tiles with replacements of differing colours. This alteration has disrupted the original symmetry of the polychromatic geometric.

It is widely acknowledged that a significant segment of the rectangular areas inlaid with tiles originates from the original design and adheres to the stylistic canon characteristic of works from the first half of the 12th century35. Original fragments, or those meticulously restored following the original scheme, are predominantly observed in the central nave (e.g., circular motifs rendered in antique green and yellow hues, as well as red porphyry) and in the side aisles (e.g., rectangular fields predominantly featuring antique green tiles and square fields with chalice-shaped floral motifs positioned in the corners of the left aisle).

In the central nave, three distinct groups of patterns are discernible along the longitudinal axis, beginning at the eastern entrance:

  1. 1.

    A rectangular field adorned with guilloche interrupted by a central cross motif.

  2. 2.

    Three square fields featuring quincunx within quincunx (geometric arrangement of five points forming a cross).

  3. 3.

    A guilloche band, extensively restored in the 17th century, leads to the altar steps.

The uniform design of the quadrilateral fields in the central nave is attributed to the pre-Cosmatesque period. In contrast, the curvilinear band decorations and their infill resemble the Roman Cosmatesque style of the 12th century35,38.

The first rectangle and the first and third squares (counting from the entrance) among the four quadrilateral areas exhibit stylistic features characteristic of the Cosmatesque tradition. In contrast, the second square reflects influences from the Cassino and Campanian schools, evident in the structural patterns and proportions of the porphyry disks. It also integrates Cosmatesque motifs attributed to the Lorenzo workshop, particularly in the style of curvilinear bands and infill decorations. The decorative elements and internal divisions of the first square correspond closely to those found in Cosmatesque floors associated with the Cosmati family35,38.

As noted by Nicola Severino, the floor of the Church of St. Chrysogonus has undergone substantial restoration. Most of the central nave’s decorative elements have been sensitively repaired, addressing missing or damaged tiles, with white marble bands replaced—these replacements, however, do not appear to date to the 12th century. Conversely, the side aisles were entirely reconstructed using a combination of original and modern materials35,38.

There is a significant correlation between the architectural design and the floor’s decorative scheme. For instance, the intersection of circular guilloche with a central porphyry slab in the rectangular field near the entrance aligns almost perfectly with the axis of the first pair of columns. Similarly, the central porphyry disk in the second square is aligned with the axis of the fifth pair of columns35. The floor is not the sole element executed in the Arte Cosmatesque style; a Cosmatesque wall tabernacle can also be found on the southern wall of the transept, near the presbytery, to the left of the entrance to the sacristy. However, likely, this was not its original location34,35.

The Basilica of Saint Chrysogonus is further distinguished by its freestanding Romanesque bell tower (Italian campanile, Fig. 7a), which dates to the 12th century37. The lower two storeys of the tower comprise a continuous wall, above which brick cornices supported by marble corbels separate five arcaded storeys. Establishing the precise date of the bell tower’s construction proves challenging. The bricks employed in its structure exhibit a slightly narrower module than those utilised in the church, suggesting that the tower may have been constructed later, potentially shortly after the basilica’s completion35.

The new Chrysogonus Basilica demonstrated departures not only from the surrounding “pagan” ancient architecture but also from contemporaneously constructed churches within the medieval Roman landscape, such as Santa Maria in Cosmedin. Krautheimer posited that Monte Cassino may have served as an inspiration for freestanding bell towers and potentially for porticoes with architraves, which Joachim Poeschke subsequently identified as quintessentially Roman features17,23.

Baroque Flair to contemporary times

The restoration of the Church of St. Chrysogonus in Trastevere was initiated by Cardinal Camillo Borghese (1552–1621), who held it as his titular church. He subsequently transferred it to his nephew, Scipione Caffarelli–Borghese (1577–1633), who continued the restoration efforts. The baroque décor of the basilica was added by Giovanni Battista Soria (1581–1651) upon the commission of Cardinal Scipione Borghese. Soria designed a new ceiling, façade, and portico15,37,39,41,42.

This period’s interior is primarily represented by the updated sections of the floor and the richly decorated ceiling, while the façade exemplifies the baroque style on the exterior. At the time, renovating old churches was considered a cardinal’s duty. As Giovanni Botero (1544–1617) suggested, it was considered nobler, more pious, and more virtuous to renovate an old church rather than to build a new one. Old churches were regarded as the cradle of Christian devotion, reflecting this belief43. It is worth noting that such renovations at that time were akin to modern-day modernisation36.

The interior of the church primarily underwent decorative changes without altering its original medieval layout. An exception to this was the reinforcement of the high windows during the installation of the ceiling. The significant weight of the richly adorned coffered ceiling necessitated modifications to the window openings in this area—initially, circular windows were replaced with square ones. The works associated with the ceiling are dated from 1618 to 1622. The ceiling is opulently adorned with gold, representing a highly costly endeavour. It is hypothesised that Borghese was engaging in a competitive display with his cardinal uncle, Aldobrandini, who had recently invested a significant sum to construct a comparable ceiling in the nearby church of Santa Maria in Trastevere36. In the central section of the wooden and gilded ceiling is a painting titled Saint Chrysogonus in Glory by Giovanni Francesco Barbieri (also known as Guercino, 1591–1666)36. This is a copy of the original painting, which was acquired by the Borghese collection in 1932 and is now housed at Lancaster House, London39,44.

The basilica also houses other artworks by notable artists, including Giovanni da San Giovanni (also known as Giovanni Mannozzi, whose paintings of angels—St. Michael, St. Gabriel, and St. Raphael—are in the second altar on the right), Cavaliere Paolo Guidotti (also known as il Cavalier Borghese; who painted two altarpieces: on the right, depicting the Crucified Christ, the Virgin Mary, and St. John, and on the left, St. Dominic and St. Francis), Giuseppe Cesari (also known as Il Giuseppino and known as Cavaliere d’Arpino; whose oil painting in the gilded dome above the ciborium depicts the Virgin Mary holding the sleeping infant Jesus), and Ludovico Gimignani (who painted a Guardian Angel in the Poli Chapel)20,41,42.

In 1623, further restoration work was initiated for the interior and façade of the church. During this period, eight side altars were added to the interior (by 1824, only four remained, including the main altar20), the floor was restored, and the Ionic capitals of the nave colonnade were reformed35,36. The floor was adorned with motifs of fantastic beasts—winged dragons and eagles—symbols of the Borghese family36. These motifs are found in seven discs within circular guilloches (intricate ornamental patterns composed of many thin, curved lines) at the end of the central nave. The dragon figures are also associated with the tradition of medieval bestiaries, and they were incorporated into the 12th-century Cosmatesque pavement38.

Cardinal Borghese’s presence is evident throughout the basilica: his coat of arms appears in the main panels of the long ceiling axis, his name is carved in the lintels of each internal door, emblems are featured in the column capitals of the side doors, amidst acanthus leaves and putti in the recessed sections of the ceiling, on the legs and top of the massive candelabrum, in the lintels and decorations of the high windows, and the frieze of the nave’s entablature, alongside numerous inscriptions. The most visible characteristic of his renovation is the presence of his name and emblems (eagles and dragons) on the façade of the basilica (Fig. 7b). Therefore, it is not an exaggeration to assert that Cardinal Borghese’s name and symbols are everywhere within the discussed church. This was not unusual at that time, as the tradition of dedicatory inscriptions had been in practice since the 15th century36.

The interior renovation also included the addition of a ciborium over the altar, designed by Giovanni Battista Soria, which was completed in 1628, as indicated by the inscription at its base. This date can be considered the conclusion of the first phase of the church’s restoration in the Baroque style. The reason for this phase was not due to the poor condition of the church—descriptions of the church testify to its good condition and beauty. The renovation, or rather a modernisation, was intended to reflect the status of Cardinal Borghese—the nephew of Pope Paul V—in the city, as well as to serve as a tangible manifestation of the excellence of the Church36. During the Baroque restoration, the medieval bell tower, which was attached to the façade on the right side of the basilica, was plastered over. It was not rediscovered until 193635.

Further changes to the interior occurred at the end of the 17th century. The culmination of the right aisle of the church is the Poli Chapel (commemorating Cardinal Fausto Poli and his family), also known as the Guardian Angel Chapel, and currently dedicated to the Most Blessed Sacrament. It was adorned according to a design by Gian Lorenzo Bernini (1598-1680), likely between 1679 and 1681, which was his last project before his death. Within the chapel, there were: an ‘Angel Guardian’ painting dated to 1680-1681 by Ludovico Gimignani (1643–1687), the depiction of the Most Holy Trinity and choirs of angels on the ceiling dated to 1675–1679 by his father Giacinto (1606–1681), and sculptures by Fausto Poli (1581–1653) and Gaudenzio Poli (1609?–1679) executed by artists from Bernini’s workshop (likely Giulio Cartari, 1642–1699), funded by Sisinio Poli (1620–1696). The original altarpiece of the Guardian Angel has been lost without a trace, now replaced by a painting created in 1848 by the Trinitarians, ‘The Trinity Crowning the Virgin, with Saints John of Matha and Felix of Valois’ (which also led to its being called the Trinity Chapel). The original appearance of the chapel, designed by Bernini, was lost due to numerous restorations20.

Between 1947 and 1950, and potentially during the 1960s, further restorations of Bernini’s chapel were undertaken. However, the specific details of these restorations are not documented due to the absence of comprehensive records. It is presumed that these may have involved most of the current gilded decorations, including the bases of the parapets, the semi-columns of the altar, the capitals, some of the entablature mouldings, and the ceiling within the side niches. In 2002, the inscription above the tympanum of Bernini’s chapel was altered from ALTARE PRIVILEGIATUM PERPETUUM to ECCE EGO VOBISCVM SVM OMNIBVS DIEBVS, and the wall surfaces were smoothed over and obscured with a uniform colour, eliminating the previous greyish-white striations. In 2003, the stained glass window was replaced with a clear one20.

The broader modernisation of the church, reflecting Baroque influences, included not only the chapel but the entire structure. In 1859 or 1866, the Cosmatesque-style floor was restored, and in the 19th century, a cross engraving was added to the rear panel of the altar35,37,38.

Chronological order of history

The basilica in question was expanded in various historical periods. Both the construction and architectural (finishing) layers have changed. The lower basilica (paleochristian church) and the upper basilica contain certain artefacts typical of a given era. For historical readability, the literature study results are presented in Table 2 and Fig. 8, which categorise the most important artefacts, features, ornaments, and construction changes in the church by historical era.

Fig. 8: Timeline of architectural transformations and historical milestones of the Basilica of Saint Chrysogonus.
figure 8

The timeline illustrates the main phases of construction and modifications, including added or changed architectural elements, with corresponding dates.Selected stages also include images of these elements.

Table. 2 Changes in the Basilica of St. Chrysogonus over the centuries

3D survey

Understanding the spatial integrity and perceptual unity of the interior hall of the Early Christian basilica is now significantly hindered by the upper basilica’s substructures and unexcavated sections, which fragment the spaces and interrupt their original connections. Massive data acquisition systems were used to digitally reconstruct these spaces, offering an opportunity to restore, in a virtual environment, the original connections of both the architectural and decorative elements.

The overall point cloud of the basilica served as a reference database for an interdisciplinary analysis of the site. In this context, the digitally navigable model serves as a research tool, providing both a comprehensive structural overview and a detailed examination of specific architectural and topographical elements. This approach systematically integrates specialised contributions from different fields into a broad and complex information system. On this topic, survey activities were designed in collaboration with art historians and architecture historians who played a fundamental role in defining the overall interpretative objectives of the 3D survey and identifying the structures’ stratigraphy to be further investigated through the digital survey.

The following analysis phase involves interpreting the three-dimensional model through 2D representations, such as orthographic projections and sectional drawings (Figs. 9 and 10). While the 3D point cloud plays a crucial role in connecting heterogeneous data to present a comprehensive image of the site, graphical synthesis, through plans, elevations, and sections, helps to structure the gathered information into thematic visualisations focused on specific aspects of the object45. On this point, integrating line drawings with thematically visualised point cloud data allows for combining qualitative elements (e.g., axis studies, geometries, and proportional relationships) with quantitative aspects (e.g., variations in elevation through point cloud colour mapping). Moreover, the integration of colour data derived from photogrammetry with the high‑precision metric measurements obtained by laser scanning (see Figs. 1014) has facilitated the production of faithful ortho‑images and two‑dimensional models at a nominal scale of 1:50.

Fig. 9
figure 9

Axonometric representation of the 3D point cloud obtained through LIDAR acquisition systems and the 2D planimetric model derived from it. (processed by the authors).

Fig. 10: Planimetric representation of the lower basilica. RGB visualisation of the point cloud with an overlay of the 2D model.
figure 10

(processed by the authors).

Fig. 11: Orthophoto of the fresco located in the apse area.
figure 11

(processed by the authors).

Fig. 12: Orthophoto of the fresco depicting the scene of the Madonna enthroned among angels, located in the eastern area of the south nave.
figure 12

(processed by the authors).

Fig. 13: Orthophoto of the fresco located in the western area of the south nave.
figure 13

(processed by the authors).

Fig. 14: Localisation of the frescoes to the global point cloud of the lower basilica.
figure 14

(processed by the authors).

The creation of 2D and 3D models, resulting from the planned and executed survey operations, is a selective process applied to an object to extract various types of information, mainly metric and colour data. Digital models support the historical study of the underground basilica of Saint Chrysogonus, both in terms of its planimetric layout and its paintings. The various tools available have enabled the development of a complex system that integrates multi-image photogrammetry from both aerial and ground perspectives with laser scanning techniques (Figs. 1517).

Fig. 15: Longitudinal section along the north side.
figure 15

RGB visualisation of the point cloud for the lower basilica and grayscale visualisation of the upper basilica. (processed by the authors).

Fig. 16: Longitudinal section along the south side of the basilica.
figure 16

Top: visualisation of the point cloud with RGB visualisation; middle: 2D drawing representation integrated with orthoimages of frescoes; bottom: 2D drawing representation (processed by the authors).

Fig. 17: Transversal sections along the west and east sides.
figure 17

On the left, RGB visualisation of the point cloud for the lower basilica and grayscale visualisation of the upper basilica; on the right, 2D drawing of the same portion and greyscale visualisation of the upper basilica (processed by the authors).

The acquisition, processing, and integration of data, though methodologically complex, represent only the foundation for the critical analysis necessary to advance knowledge of the structure. The digital model generated from the survey operations allowed for the systematic organisation of spatial relationships between different areas and the formulation of hypotheses regarding their original configuration. From an interpretative perspective, this approach facilitated the verification of floor-level variations.

Specifically, in the southeastern section of the Early Christian structure, now bounded by modern substructures and the counter-façade wall of the basilica, remnants of the scene of the Madonna Enthroned with Angels can be observed on the southern wall. The original floor level is distinguishable in this area, identified through surviving floor fragments. Along the same southern wall, in the adjacent nave, three distinct floor levels can be identified, with an overall height difference of approximately one metre between the lowest section (toward the east) and the highest (toward the west), where frescoes of draperies and saintly portraits within roundels are located. The floor level in the area with the Madonna Enthroned fresco aligns with the highest level of the adjacent nave, providing insights into the basilica’s original floor plan (Fig. 17).

Regarding the relative elevations between spaces, another key observation concerns the substantial alignment, on three distinct levels, between the southern and northern sections of the basilica. This relationship, clearly visualised through the elevation map derived from the numerical model, highlights the spatial continuity between these areas, which, despite being interrupted by later substructures, originally formed a single unified space. Another interpretative approach enabled by the integrated mass survey is the verification of planimetric alignments. In this regard, visible discontinuities in the standing walls sometimes correspond to detectable variations in structural orientation. This type of integrated analysis enables a deeper understanding of the relationship between the basilica and the pre-existing structures connected to it.

Discussion

This study is innovative in that it presents a combined case-study approach, integrating critical analysis of historical sources with the application of advanced digital technologies. While a number of studies have addressed the use of such technologies in the context of cultural heritage2,46,47,48,49, the present work stands out through its interdisciplinary methodology applied to a specific and historically complex architectural site.

Photogrammetric techniques have facilitated the verification of architectural modifications identified in the historical analysis. The critical and interpretative considerations mentioned here were conducted by exploring and querying the virtual model within a three-dimensional environment. However, this led to the need to investigate representation strategies capable of translating and condensing such information into synthetic graphical outputs. To achieve this, the 2D models—created using a standardised graphical coding system established within the field of archaeological architecture—were complemented by a two-dimensional contour line representation.

This approach, partially derived from traditional large-scale cartography and partially from the representation of rock-cut architecture, proved to be well-suited to the intended objectives for several reasons. The most significant aspect is the process involved in generating this type of 2D model: the discretisation of the point cloud, which isolates certain elevation values according to a defined interval, followed by the generation of 2D contour polylines. This process is scientifically reproducible and parameterizable, ensuring that the acquired data remains in its original configuration without undergoing interpretative transformations. At the same time, however, selecting a specific interval between contour lines—determined by the specialist according to their objectives—enables a critical reading of the object to be applied and communicated.

In the context of archaeological architecture, this combination serves as an essential foundational dataset for site documentation and transmission. From an application perspective, contour line representation does not eliminate the morphological three-dimensionality of the object but rather enhances it by introducing a fixed rule—a parameter expressed by the height difference between two consecutive lines. The effect accentuates irregularities in floor levels, emphasising elevation changes and predominant spatial orientations.

This method integrates well with the interpretative drawing of the object, the actual 2D model, highlighting the multiple characteristics and methodological themes inherent to archaeological architecture. To derive contour lines from the point cloud, it was necessary to create a Digital Elevation Model (DEM). A DEM is a statistical surface that assigns an elevation (Z) to each pair of X and Y coordinates, constructed by discretising the topographic surface through a square grid. Each square represents a portion of a horizontal plane, defined by four vertices (with known X and Y coordinates), and has an elevation (Z value) typically equal to the average elevation of all points within its perimeter. The DEM output appears as a more or less pixelated image, depending on the grid size. The smaller the grid step, the more accurately the surveyed object is represented.

For the discretisation of the model, a square grid of 10 × 10 cm was used, ensuring a high level of detail even for the crests of the preserved wall remnants. The grid cell size is crucial, especially for generating contour lines. If the grid cells are too small, the DEM will closely approximate the point cloud; however, the contour lines may become excessively jagged, capturing minor, localised details or even producing artefacts that should not be included in the 2D model. Conversely, if the grid cells are too large, the contour lines may appear smoother but risk omitting significant architectural features such as niches or structural elements.

After several trials, a contour interval (step) of 10 cm was selected to effectively represent both the subtle floor variations and the wall remnants preserved just a few centimetres above ground level. Each contour line was defined as a polyline with a certain level of complexity. The resulting graphical output was overlaid onto the previously produced plans, providing a synchronic view of the spatial characteristics of the lower basilica of Saint Chrysogonus (Fig. 18).

Fig. 18: Elevation map.
figure 18

Planimetric visualisation of the lower basilica with colour characterisation referring to floor levels (DEM) and contour lines. (processed by the authors).

The comparison between the two outputs—the one generated through critical interpretation of the point cloud and the one based on the automated extraction of contour lines—highlights issues related to the representation process as a means of analysis (Fig. 19). Specifically, while the interpretative approach to 2D modelling enables prolonged and detailed examination of the object and its properties, non-interpretative graphical outputs serve as a neutral reference point for interdisciplinary reflection. In this case, the initial analysis phase relied on non-interpretative representations, allowing each researcher to develop an independent understanding of the object. However, after this essential step, the second analysis phase involved the graphical restitution of significant elements, allowing the model to incorporate and communicate critical observations.

Fig. 19: Top: 2D planimetric model of the lower basilica. Bottom.
figure 19

planimetric visualisation with contour line representation at 10 cm intervals. (processed by the authors).

The methodological approach based on the processing and multi-scale analysis of models has once again proven to be a valuable tool for an interdisciplinary study of the site. Specifically, the immediacy of exploration and query ability make these digital models indispensable for understanding the structure, serving as a shared data foundation across various specialised fields that traditionally rely on widely different interpretative systems. The added value of such models lies precisely in their ability to connect these sector-specific perspectives within a system where the contribution of individual expertise is crucial for achieving a comprehensive understanding50.

In this study, a cross-analysis approach was adopted, as illustrated in the flowchart (Fig. 3), integrating insights from the historical literature review with data obtained through digital tools, including laser scanning and photogrammetry. This approach operates bidirectionally: the digital survey results inform the development of research hypotheses, while historical sources and previous studies provide essential context and validation for observations derived from modern measurement techniques. The complementary nature of these methods is crucial: neither approach alone could provide a comprehensive understanding of the basilica. By integrating both lines of evidence, the research achieves a mutually reinforcing process, where digital and documentary analyses continuously inform and validate each other. This synergy enhances the robustness and reliability of the results, fostering a more comprehensive understanding of the site and enabling interdisciplinary conclusions that would not be achievable with a single method alone.

In the case of the lower Basilica, the research concerned valid reconstruction hypotheses directly influenced the modelling process, particularly in determining representation strategies for different elements. The choice of these strategies directly impacts the level of detail that can be visualised. For example, creating a three-dimensional model with a “neutral” surface treatment, without any texture characterisation related to surface materials or state of conservation, enhances the perception of architectural space, materialising the reconstructed volume of the architecture in contrast to the traces revealed by archaeological analysis. At the same time, this type of model serves as an intuitive and interpretive tool for scholars less accustomed to reading technical models. Moreover, such a model is naturally suited to receiving various characterisation forms—mainly derived from photogrammetry—further refining its role as an interpretative reconstruction tool.

Following the same rationale, the decision to incorporate contour lines, both horizontal and vertical, as well as the selection of an appropriate interval to facilitate overall readability, emerged from a collaborative effort among different fields of expertise. Lastly, the models produced have enabled the visualisation of the structure from unconventional perspectives, drawing attention to details that might otherwise remain imperceptible or insufficiently explored during site inspections or direct analyses.

Further development of the research could involve creating a virtual twin of an object, which can contain various types of data, such as the results of numerical calculations51,52, the identification and dating of frescoes, as well as the technical condition remarks and evaluation of observed damages. Structure from Motion (SfM) contributes to the development of virtual twins by enabling the generation of precise three-dimensional reconstructions and accurate terrain representations. Together with a digital elevation model, enable cost-effective creation and ongoing updating of these virtual models. This complex approach will facilitate making the right decisions regarding intervention works and eliminate errors during restoration53, ensuring the safe use of the basilica for years to come.

Among the elements subjected to detailed analysis, particular attention was paid to the polychrome wall paintings. The photogrammetric data enabled enhanced visualisation and comparison of pigments, even in areas where the original frescoes are partially degraded. Therefore, a calibrated photogrammetric pipeline supported accurate colour rendering was needed. This aspect becomes crucial when dealing with those archaeological areas with heterogeneous lighting sources and articulated spaces. In these conditions, photogrammetry plays a key role, giving the possibility to create a proper lighting set for each surface to ensure colour accuracy.

To fully understand the original polychrome schemes and their transformations across successive phases of use and conservation, it would be essential to carry out specialised material investigations. Analytical techniques such as Raman spectroscopy, macro X-ray fluorescence (MA-XRF) elemental mapping, multispectral scanning reflectography, fibre optics reflectance spectroscopy (FORS) or infra-red reflectography (IRR)—widely adopted in the study of wall paintings54,55,56,57,58—could offer non-invasive identification of the materials employed, their application techniques, and any later interventions or overpainting.

In addition, laser-induced fluorescence (LIF) could be employed to assess pigment composition and the presence or degradation of fixatives. This technique has been successfully applied as a non-invasive, real-time diagnostic tool for the analysis of historic artworks59, and could provide valuable insights for conservators in planning and executing future conservation treatments.

Incorporating the results of these investigations into the digital dataset would greatly enhance the interpretative capacity of the model, forming a foundation for the development of a full digital twin of the site, combining geometric and material information. As highlighted in recent publications60,61,62, this kind of multidisciplinary integration is currently among the most promising approaches for the documentation and conservation of architectural heritage. This constitutes a valuable basis for future research.