# Spatial distribution of mineral development in Carboniferous Bowland Shale, UK at 3D micro- to nano-scales

Jingyue Hao, Lin Ma, Cathy Hollis, Anne-Laure Fauchille, Kevin Taylor

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Jingyue Hao, Lin Ma, Cathy Hollis, Anne-Laure Fauchille, Kevin Taylor. Spatial distribution of mineral development in Carboniferous Bowland Shale, UK at 3D micro- to nano- scales. International Journal of Coal Geology, 2023, 271, pp.104236. 10.1016/j.coal.2023.104236. hal-05092854

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# Spatial distribution of mineral development in Carboniferous Bowland Shale, UK at 3D micro- to nano- scales

Jingyue Hao<sup>a</sup>, Lin Ma<sup>b, *</sup>, Cathy Hollis<sup>a</sup>, Anne-Laure Fauchille<sup>c</sup>, Kevin G. Taylor<sup>a</sup>

<figure><img src="image_3.png" /></figure>

## ARTICLE INFO

**Keywords:**

Bowland Shale

Diagenesis

Paragenetic sequence

XCT

$CO_2$ sequestration

## ABSTRACT

Determination of mineral texture and diagenetic features in mudstones is crucial to reveal the history of their pore systems and provides key information to predict their future sealing ability, reactivity and storage capacity for sequestered $CO_2$, hydrogen storage or nuclear waste disposal. To understand the spatial transport and storage of fluids, it is necessary to map the distribution of minerals and fractures in three dimensions (3D). This study proposes a novel, multi-scale three-dimensional (3D) imaging method, i.e., a combination of synchrotron-sourced micro-x-ray tomography and lab-sourced nano-tomography, to investigate the sedimentology and diagenetic features of the Bowland Shale, one of the most volumetrically important mudstone-dominated systems in the UK. Diagenetic minerals have been identified and characterised, including pyrite, calcite, kaolinite, illite, chlorite, dolomite, ankerite and authigenic quartz (micro-sized quartz and quartz overgrowths). Multi-scale 3D images provide detailed information about dolomite-ankerite zonation and carbonate dissolution pores. These features cannot be observed or quantified by conventional 2D methods, and they have not been reported in this subject area before. Using these results, potential reactions during carbon storage and other subsurface storage applications are predicted.

## 1. Introduction

Mudstone, a fine-grained sedimentary rock, consists mostly of clay- or silt-size particles (Lazar et al., 2015), and may possess fissility (Aplin and Macquaker, 2011). In petroleum systems, mudstone can serve as a source, reservoir and seal for conventional and unconventional hydrocarbon (Aplin and Macquaker, 2011). Due to its low permeability, mudstone is also considered to be a potential caprock or host rock for long-term carbon dioxide storage, hydrogen storage and nuclear waste disposal (Marschall et al., 2005; Delage et al., 2010; Armitage et al., 2013, 2016; Ma et al., 2021a). For example, 38 trillion cubic metres of the Bowland Shale in the UK have been estimated to have 47.5–49.5 Gt carbon storage capacity (Ma et al., 2021a). Understanding the nature of mudstones is important for assessing the sealing capacity and leakage risks of permeant carbon storage.

Over the past two decades, many studies have been undertaken on mudstone depositional processes and fabrics, petrographic characteristics, rock mechanics and permeability (Macquaker and Gawthorpe, 1993; Dewhurst et al., 1999; Macquaker et al., 2007; Schneider et al.,

2011; Lazar et al., 2015). Mineralogy plays an important role in the physical properties of mudstones, such as brittleness and permeability (Peltonen et al., 2008, 2009; Baruch et al., 2015). For example, kaolinite-rich samples have a lower permeability than silt-rich samples after compaction due to their higher clay alignment (Mondol, 2009). Illite has a greater charge than smectite and is more prone to react with pore fluids and exchange cations, thereby affecting mudstone porosity and permeability (Wilson et al., 2016). Under geological carbon capture and storage operation, $CO_2$ will be compressed into a dense fluid and injected into the subsurface. The increase in $CO_2$ fluid pressure may increase a caprock's permeability (Armitage et al., 2013). Calcite and dolomite are the most reactive minerals to $CO_2$-brine-rock interactions (Credoz et al., 2009). The dissolution of calcite-cemented zones can increase the porosity of caprocks (Pearce et al., 2019) and may increase leakage risks from carbon storage reservoirs through the caprock following injection (Worden et al., 2020). Other minerals, such as K-feldspar and chlorite, may dissolve as well (Gaus et al., 2005; Jayasekara et al., 2020). Meanwhile, new carbonate and clay minerals such as ankerite and kaolinite may precipitate during interactions (Gaus et al.,

<footnote><sup>a</sup> Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, UK</footnote>

<footnote><sup>b</sup> Department of Chemical Engineering, The University of Manchester, Manchester M13 9PL, UK</footnote>

<footnote><sup>c</sup> Centrale Nantes, Institut de recherche en Génie civil et Mécanique (GeM) – UMR CNRS 6183, 1 rue de la Noë, Nantes Cedex 3 44321, France</footnote>

<footnote>* Corresponding author at: Department of Chemical Engineering, The University of Manchester, Manchester M13 9PL, UK.
E-mail address: lin.ma@manchester.ac.uk (L. Ma).</footnote>
<table><caption>**Table 1**
The details of studied samples and their lithologies, cited from Fauchille et al. (2017).</caption><thead><tr><th rowspan="2">Samples</th><th rowspan="2">Depth (m)</th><th rowspan="2">Lithofacies</th><th colspan="7">Mineral composition (wt%)</th><th rowspan="2">TOC (wt%)</th></tr><tr><th>Kaolinite</th><th>Quartz</th><th>Calcite</th><th>Ankerite</th><th>Pyrite</th><th>Muscovite</th><th>Albite</th></tr></thead><tbody><tr><td>B1</td><td>2073.34</td><td>Unlaminated quartz-rich</td><td>0</td><td>58</td><td>15</td><td>13</td><td>2</td><td>9</td><td>3</td><td>1.4</td></tr><tr><td>B2</td><td>2081.27</td><td>Transition un- to interlaminated quartz-rich</td><td>5</td><td>53</td><td>17</td><td>1</td><td>8</td><td>11</td><td>5</td><td>4.1</td></tr><tr><td>B4</td><td>2089.83</td><td>Unlaminated quartz-rich</td><td>5</td><td>65</td><td>4</td><td>5</td><td>4</td><td>11</td><td>6</td><td>1.7</td></tr><tr><td>B5</td><td>2091.69</td><td>Interlaminated quartz-rich</td><td>6</td><td>56</td><td>12</td><td>6</td><td>6</td><td>10</td><td>4</td><td>3.2</td></tr><tr><td>B6</td><td>2344.70</td><td>Unlaminated quartz-rich</td><td>7</td><td>71</td><td>6</td><td>2</td><td>1</td><td>10</td><td>3</td><td>6.1</td></tr><tr><td>B7</td><td>2488.84</td><td>Interlaminated quartz-rich</td><td>3</td><td>68</td><td>10</td><td>3</td><td>2</td><td>10</td><td>4</td><td>1.5</td></tr><tr><td>B8</td><td>2495.27</td><td>Laminated quartz-rich</td><td>18</td><td>52</td><td>3</td><td>113</td><td>2</td><td>5</td><td>9</td><td>1.1</td></tr><tr><td>B9</td><td>2496.92</td><td>Unlaminated quartz-rich</td><td>6</td><td>52</td><td>21</td><td>1</td><td>5</td><td>9</td><td>4</td><td>2.1</td></tr><tr><td>B10</td><td>2500.49</td><td>Unlaminated quartz-rich</td><td>5</td><td>56</td><td>18</td><td>2</td><td>5</td><td>10</td><td>5</td><td>2.0</td></tr></tbody></table>

<figure><img src="image_4.png" /><figcaption>**Fig. 1.** The location of the Preese Hall-1. (a) The map of UK with the study area marked. (b) The location of Preese Hall-1 borehole, modified after Waters et al. (2009). BH: Bowland High; BS: Bowland Sub-basin; CLH: Central Lancashire High; RB: Rossendale Basin; HdB: Huddersfield Basin; AB: Askrigg Platform; MWB: Market Weighton Block; GT: Gainsborough Trough; HH: Holme High; HS: Hathern Shelf; DP: Derbyshire Platform; EG: Edale Gulf; WG: Widmerpool Gulf; EMS: East Midlands Shelf.</figcaption></figure>

2005; Alemu et al., 2011).

Optical and scanning electron microscopy has been applied extensively to investigate the mineralogy and porosity of mudstones (Schieber et al., 2000; Aplin and Macquaker, 2011; Macquaker et al., 2014; Liu et al., 2019; Dowey and Taylor, 2020; Hao et al., 2021). These techniques, however, are limited to 2D observations of mineral features and relationships. In contrast, 3D images allow the internal and spatial characteristics of an object to be observed. Heath et al. (2011) used dual-beam focused ion beam-scanning electron microscopy (FIB-SEM) to characterise pores in 3D and categorize them in seven types. Ma et al. (2016, 2017, 2018) combined micro- and nano-CT to observe the microstructure, morphology of pores and pore-network in mudstones and identified four types of organic-related and mineral-related pores. These studies worked mainly on the pore system. Robinet et al. (2012) combined 2D (SEM) and 3D (micro-CT) images to map major mineral phases in the Callovian-Oxfordian mudstone from the Bure, France. They mostly focused on the mineral distribution and its effect on solute transfer in clay-rich rocks. Few studies have combined micro and nano-scale methods to study mineral characteristics in mudstones, sandstones and limestones. This study integrates 2D (optical and SEM microscopy)

and 3D observations (X-ray micro- and nano-CT) to characterise and quantify mineral textures, as well as related pores, in the Carboniferous Bowland Shale, UK. The aims of this study are to: i) characterise the textures of minerals in 2D and 3D within the mudstone; ii) understand how they formed during diagenesis and iii) investigate their potential impact on CO₂ sequestration.

## 2. Samples and geological background

Nine samples were collected from the Bowland Shale Formation at measured depths ranging from 2073.34 to 2500.49 m (datum in rotary table with the elevation of 12.9 m) in the Preese Hall-1 borehole in the Bowland Basin, UK (Table 1). The Bowland Basin is a NE-SW-trending fault-controlled graben that was established in late Devonian/Tournai-sian due to regional back-arc extension (Gawthorpe, 1987). It is located to the south of Askrigg Platform and to the north-west of the Central Lancashire High. The Bowland Shale Formation encountered in Preese Hall-1 is upper Visean in age (Fig. 1) and consists of mudstones and interbedded sandstones and carbonates (Clarke et al., 2018).
<figure><img src="image_5.png" /><figcaption>Fig. 2. Examples of mineral identification using EDS spectra, maps and quantification. Sample B8 (left), 2495.27 m and sample B5 (right), 2091.69 m.</figcaption></figure>

## 3. Methods

### 3.1. Petrographic and microbeam analysis

Polished thin sections with 30 µm thickness were made for each

sample and observed under transmitted light using a Nikon Eclipse LV100NPOL microscope equipped with a Nikon DS-Fi2 camera. Thin sections were placed in a high vacuum chamber and bombarded with 15 kV using a CITL 8200Mk5-2 cathodoluminescence microscope equipped with a ProgRes software. A FEI Quanta 650 SEM equipped with a back-
<figure><img src="image_6.png" /><figcaption>Fig. 3. The comparison of 2D SEM images and 2D CT slices from 3D image datasets. 2D SEM images can be used to help identify minerals in CT images by their gray values and morphologies. (a) Dolomite, ferroan dolomite and ankerite in BSE image, sample B8, 2495.27 m. (b) Dolomite, ferroan dolomite and ankerite in 2D slice from 3D image dataset, sample B5, 2091.69 m. (c) Muscovite in BSE image, sample B8, 2495.27 m. (d) Muscovite in 2D slice from 3D image dataset, sample B6, 2344.70 m.</figcaption></figure>

scattered electron detector, with an electron beam energy of 15 kV was used to acquire Backscattered electrons (BSE) images. The Energy-dispersive X-ray spectroscopy (EDS) analysis was performed on a Quantax Esprit software. Element maps of selected areas of interest and spectra of selected points were obtained using a Bruker EDS detector.

## 3.2. Synchrotron sourced micro-scale X-ray computed tomography (synchrotron Micro-CT)

Synchrotron-source micro-scale X-ray computed tomography (synchrotron Micro-CT) was carried out in the I13 Beamline (MT15506-1) at the Diamond Light Source, UK, with a pink beam. Samples were cut into 2 × 2 × 10 mm³ cubes. The energy used was 20 kV with a 0.04 s exposure time. The voxel size of the resulting images is 1.6 µm.

## 3.3. Lab-sourced nano-scale X-ray computed tomography (nano-CT)

Lab-source nano-scale X-ray computed tomography (nano-CT) was conducted using a Zeiss Ultra 810 scanner at the University of Manchester Henry Moseley X-ray Imaging Facility. Samples were cut into 60 µm diameter cylinders using a laser cutter (3D Micromac MicroPREP TM system equipped with a 532 nm diode-pumped solid state picosecond laser). The energy used was 8 kV with a 160 s exposure time. The resulting voxel size is 64 nm.

## 3.4. Image analysis

### 3.4.1. 2D image analysis

Minerals in 2D BSE images were identified using EDS maps and spectra. Some examples are given below. The contents of calcium, magnesium and iron in spectra were used to discriminate dolomite, ferroan dolomite and ankerite (Fig. 2a-d). Dolomite is mainly composed of calcium (31.9 wt%) and magnesium (13.8 wt%). Ferroan dolomite (Mg > Fe) contains higher iron and lower magnesium than dolomite. The iron content is relatively higher in ankerite (Mg < Fe) than ferroan dolomite. Spectra and quantification show an increase in iron content from dolomite to ankerite. EDS maps also provide detailed information of elemental composition of minerals. Figs. 2e-h show that kaolinite is predominantly composed of silicon and aluminium.

### 3.4.2. Micro- and nano-CT image analysis

In 3D images, minerals were discriminated by their grayscale and morphologies (Madonna et al., 2012; Sun et al., 2020). In grayscale, pyrite has the highest value and followed by the carbonate. Silicate minerals have relatively lower values. Also, ankerite is brighter than dolomite and calcite owing to its higher content of iron. From morphologies, dolomite usually shows a rhombic shape while ankerite is irregular in shape. Calcite is irregular but does not have clear mineral margins. Figs. 3a-b show dolomite, ferroan dolomite and ankerite in 2D SEM image and 2D CT slice. Some phyllosilicates (i.e., muscovite) can be discriminated in nano-CT images. Figs. 3c-d show muscovite in 2D SEM image and 2D CT slice, respectively. They can be discriminated using
<figure><img src="image_7.png" /><figcaption>Fig. 4. Diagenetic clay minerals in the studied samples. (a) Kaolinite cements within the intraskeletal porosity, sample B5, 2091.69 m. (b) The EDS spectrum of kaolinite, (c) Chlorite, sample B9, 2496.92 m.. (d) The EDS spectrum of chlorite, sample B9, 2496.92 m. K: kaolinite; Chl: chlorite; Qz: quartz; Cal: calcite.</figcaption></figure>

their mineral morphologies and boundary in segmentation. For clay minerals such as kaolinite cements, they can be discriminated when they occur within the intraskeletal porosity. In this case, kaolinite cements were discriminated using their gray values and morphologies of skeleton. Other clay minerals such as illite and chlorite are commonly present in the matrix. However, they are difficult to be discriminated in 3D images due to their small size, unclear boundaries and similar gray values.

### 3.5. 3D images processing steps

#### 1) Noise reduction.

Images were processed using Avizo 2020.3.1 (Thermo Fisher, USA). A non-local means filter with the spatial standard deviation of 3, intensity standard deviation of 0.3, search window pixel of 10 and local neighbourhood pixel of 5 was applied to reduce image noise.

#### 2) Segmentation.

Three methods were used for the segmentation of different materials in images, including magic wand, threshold and watershed. Magic wand was used to select specific minerals. Magic wand is referred as a 'region-growing' tool in Avizo. When an individual 'seed voxel' of material is selected, the largest connected area containing the voxel and all voxels with gray values within a specified range is selected (Forst et al., 2014). Hence, magic wand was applied to 'all slices' and 'same materials only' for selecting specific features or individual mineral in 3D images (Curtis et al., 2014). Threshold was used to select different materials in the studied samples. Watershed was commonly used to confirm the boundaries of different materials (i.e., the boundary between pyrite and dolomite). It was used after the selection of specific materials.

#### 3) Measurement.

The measurement of pore size was performed after segmentation using label analysis module, including equivalent diameter, sphericity, length3d, width 3d, area3d, volume3d and thickness3d. Equivalent diameter (EqDiameter) is given by the formula as follows (Scientific, 2019):

$$EqDiameter = \sqrt[3]{\frac{6 \times Volume3d}{\pi}}$$

### 4. Results

#### 4.1. Authigenic clay minerals

Kaolinite and chlorite are found in Bowland Shale samples. They might have diagenetic as well as detrital origins. BSE images were used to distinguish clay minerals formed during diagenetic alterations. Authigenic kaolinite is typically found as a cement within intraskeletal porosity, which is defined as skeleton of marine organisms preserved after inside soft tissue decomposition (Fig. 4a, b). Authigenic chlorite is present in the matrix (Fig. 4c, d)

#### 4.2. Pyrite

Pyrite occupies 1–8 wt% of the total mineral content (Fauchille et al., 2017). SEM images show that pyrite takes framboidal and euhedral forms in the Bowland Shale. Framboidal pyrite is sub-spherical and closely packed (Fig. 5a). The diameter of framboidal pyrite is typically below 10 µm. The morphology of framboidal pyrite aggregates is visible in 3D micro-CT images (Fig. 5c, d). Framboidal pyrite crystals in the aggregate are spherical and connected to one another (Fig. 5d). Inter-
<figure><img src="image_8.png" /><figcaption>**Fig. 5.** Pyrite in the Bowland Shale samples. (a) Framboidal pyrite and aggregate of euhedral pyrite, sample B8, 2495.27 m. (b) Euhedral pyrite within the dolomite and calcite, sample B5, 2091.69 m. (c) Aggregate of framboidal pyrite in the matrix, sample B1, 2073.34 m. (d) 3D reconstruction of framboidal pyrite and inter-mineral pores around it, sample B1, 2073.34 m. (e) A mass of pyrite crystals and intra-mineral pore. The Eqdiameter of this selected intra-pyrite pore is 67 µm, sample B8, 2495.27 m. (f) 3D reconstruction of pyrite and intra-mineral pore, sample B8, 2495.27 m.</figcaption></figure>

mineral pores are present between framboidal pyrite crystals. The EqDiameter of these pores were measured (min: 4 µm; max: 47 µm; mean: 12 µm; SD: 8 µm). Intra-mineral pores in a mass of pyrite crystals can be observed in 3D images (Fig. 5e, f). The EqDiameter of intra-mineral pores ranges from 3 to 67 µm (mean = 15 µm, SD = 11 µm). Euhedral pyrite is present and has a good crystal shape. It is sometimes enveloped by

dolomite and calcite (Fig. 5b).

### 4.3. Quartz

Authigenic quartz in the Bowland Shale samples has two forms: micro-sized quartz and quartz overgrowth. Micro-sized quartz is
<figure><img src="image_9.png" /><figcaption>**Fig. 6.** Quartz in the Bowland Shale samples. (a) Micro-sized quartz in the Bowland Shale sample, sample B7, 2488.84 m. (b) The EDS map of micro-sized quartz, sample B7, 2488.84 m. (c) Micro-sized quartz in the matrix, sample B8, 2495.27 m. (d) A high magnification image of quartz overgrowth between two detrital quartz grains. Intra- mineral pores are common in detrital quartz grains, sample B5, 2091.69 m. (e) A 2D slice of micro-sized quartz, sample B6, 2344.7 m. (f) 3D reconstruction of micro-sized quartz as well as pores around them. Pyrite occurs within the micro-sized quartz. Pores are represented in red, sample B6, 2344.7 m. Qz: quartz; Si: micro-sized quartz; D: dolomite; Cal: calcite. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)</figcaption></figure>

abundant in quartz-rich samples with the quartz content ranging from 52 to 71 wt% (Fig. 6a-c). Micro-sized quartz is commonly intergrown with other minerals (i.e., kaolinite, pyrite and calcite) (Fig. 4a). They can clearly be observed in nano-CT images (Fig. 6e). Based on measurement in 3D images, the length of micro-sized quartz ranges in size from 36 to 102 µm (mean = 78 µm, SD = 24 µm). The width of micro-sized quartz ranges in size from 10 to 39 µm (mean = 31 µm, SD = 9 µm). Pores are present in and around them (EqDiameter min: 1 µm; max: 22 µm; mean: 4 µm; SD: 3 µm) (Fig. 6f). Framboidal pyrite is enveloped by micro-sized quartz (Fig. 6f). Based on 3D images, pyrite and silica partially fill primary pores (Fig. 5d, f and 6f). Some quartz cements occur as a syntaxial overgrowth (<1 µm) on detrital quartz and they partly coat the grain (Fig. 6d).

### 4.4. Dolomite and ankerite

Dolomite and ankerite account for 2–13 wt% of the total mineral composition of the studied samples (Fauchille et al., 2017). Non-ferroan dolomite in the studied samples mostly has a rhombic shape (Fig. 7a). Euhedral pyrite is enclosed in non-ferroan dolomite in some cases (Fig. 7b). In the example shown in Fig. 7c, there are some calcite remnants in non-ferroan dolomite. Non-ferroan dolomite, ferroan dolomite and ankerite were present and show zoning (Fig. 7a). Ferroan dolomite takes the form of an overgrowth on the dolomite (Fig. 7a). Ankerite seems to have precipitated around quartz (Fig. 7d). Small dolomite and ankerite inclusions are also present in micro-sized quartz (Fig. 6a). In Fig. 8a, the ankerite envelops the detrital quartz. In Fig. 8b, the same quartz with a clear boundary was adjacent to the ankerite. In 3D, it is clear that ankerite did not precipitate around the quartz, but rather
<figure><img src="image_10.png" /><figcaption>**Fig. 7.** Backscattered electron images of dolomite and ankerite in the studied samples. (a) Non-ferroan dolomite and its ferroan dolomite and ankerite outgrowths. Most of dolomite crystals have a rhombic shape. Zoning is occasionally present in some of the studied samples. Sample B8, 2495.27 m. (b) Euhedral pyrite within the dolomite, sample B5, 2091.69 m. (c) Non-ferroan and ferroan dolomite with some calcite remnants, sample B5, 2091.69 m. (d) Ankerite and its associated quartz. Sample B9, 2496.92 m. D: non-ferroan dolomite; FD: ferroan dolomite; Ank: ankerite; Py: pyrite; Qz: quartz; Cal: calcite.</figcaption></figure>

formed in the space between quartz (Fig. 8c). Some small quartz inclusions (<10 µm) can be seen and are enclosed within the ankerite (Fig. 8d).

Zonation within dolomite and ankerite was observed in 3D images (Fig. 9a-e). An entire non-ferroan dolomite crystal was reconstructed and its spatial morphology shows a rhombic shape with a length of approximately 150 µm (Fig. 9b). Ferroan dolomite is in contact with non-ferroan dolomite (Fig. 9c) and ferroan dolomite shows an outer surface with irregular cavities (Fig. 9c). Ankerite is partially in contact with non-ferroan dolomite and ferroan dolomite (Fig. 9d, e). Ferroan dolomite and ankerite dissolution was observed in 3D images. There are some pores within carbonate phases with diameters of approximately 200 µm (Fig. 9f, g) and some ankerite remnants and pyrite can be observed in the pore (Fig. 9f, i). Organic matter (bitumen) sometimes fills these pores (Fig. 9h, j).

There are three types of pores related to the carbonate phases in the studied samples: i) intra-mineral pores; (ii) inter-mineral pores and (iii) carbonate dissolution pores (Fig. 10a-d). Some inter-mineral pores are elongate and others are subrounded, ellipse and irregular (Fig. 10c). The *EqDiameter* of inter-mineral pores ranges in size from 2 to 109 µm (mean = 14 µm, SD = 10 µm). Their length ranges from 2 to 491 µm (mean = 33 µm, SD = 37 µm). They are 2–151 µm in width (mean = 13 µm, SD = 11 µm). Intra-mineral pores are subrounded or ellipsoid in shape and range in *EqDiameter* from 4 to 21 µm (mean = 8 µm, SD = 3 µm) (Fig. 10d, h). Their length is in the range of 6–56 µm (mean = 14 µm, SD = 8 µm). Their width is 4–20 µm (mean = 8 µm, SD = 3 µm). Carbonate dissolution pores cannot be discriminated in 2D images but they can clearly be discriminated in 3D images. Fig. 10i displays the geometry of carbonate dissolution pores, whilst Fig. 10e shows the intra-

part of the carbonate dissolution pore. In this selected 2D slice, pores occur within the ankerite (Fig. 10e and i). As the slice is moved to approximate 50 µm from the sample top, the internal part of the carbonate dissolution pore is displayed (Fig. 10g-i). The *EqDiameter* of carbonate dissolution pores is in the range of 15–61 µm (mean = 35 µm, SD = 18 µm). They are 28–154 µm in length (mean = 81 µm, SD = 47 µm). They are 14–84 µm in width (mean = 39 µm, SD = 26 µm). Compared to inter-mineral pores and intra-mineral pores, carbonate dissolution pores have the largest average *EqDiameter*, length and width.

### 4.5. Calcite

There are two phases of calcite cements. Fig. 4a depicts the first phase of calcite cements, which was replaced by micro-sized quartz. The second phase of calcite cements is shown in Fig. 11a, which replaced albite in some cases. Sometimes they are also intergrown with ferroan dolomite (Fig. 11a). Pores are also abundant within calcite cements (Fig. 11b). Calcite-filled veins are present in some Bowland Shale samples (i.e. samples B6 and B8) and display high angles to the bedding, approximate 60° to 80° (Fig. 11c). All of these calcite-filled veins show dull orange cathodoluminescence (Fig. 11d). Chlorite has commonly replaced calcite around the vein walls (Fig. 11e). Bitumen-filled veins crosscut both calcite-filled veins and chlorite (Fig. 11f).

## 5. Discussion

### 5.1. Diagenetic development in the Bowland Shale

The interpreted paragenetic sequence of diagenesis of the Bowland
<figure><img src="image_11.png" /><figcaption>**Fig. 8.** The 3D reconstruction of carbonates and their surrounding minerals, sample B1, 2073.34 m. (a) A 2D slice of quartz and ankerite. Quartz was enclosed in the ankerite. (b) Same sample but different 2D slice of quartz and ankerite. The same quartz was adjacent to the ankerite. (c) The 3D relationship between quartz and ankerite. Ankerite was precipitated in the space between quartz. The red arrow shows the boundary between them. (d) Some quartz inclusions within the frame, which are enclosed in the ankerite. The white area (transparent area) is the area of carbonates shown in Fig. 6c. Cal: calcite; Ank: ankerite; Qz: quartz. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)</figcaption></figure>

Shale is shown in Fig. 12. The Bowland Shale samples were buried to approximately 3.65 km during the late Carboniferous, and have therefore undergone deep burial diagenesis, before the basin was inverted (de Pater and Baisch, 2011). Kaolinite is more abundant in the laminated quartz-rich sample B8 (18 wt%) compared to other, unlaminated, samples, according to the XRD measurements (Fauchille et al., 2017). Euhedral pyrite is present within non-ferroan dolomite, indicating that it was formed prior to non-ferroan dolomite (Fig. 7b).

The second phase of calcite cementation is intergrown with ferroan dolomite and seems to have precipitated simultaneously or after ferroan dolomite (Fig. 11a). The dissolution of ferroan dolomite and the precipitation of ankerite were observed in our study within zoned dolomite-ankerite crystals. Based on the 3D data, the cavities formed on the surface of ferroan dolomite with the non-ferroan dolomite remaining well-preserved. Ferroan dolomite is present between dolomite and ankerite and in contact with non-ferroan dolomite. As a result of the dissolution of ferroan dolomite and the subsequent precipitation of ankerite, ankerite is in contact with non-ferroan dolomite. The relationship between ankerite and quartz is clearer in 3D images than 2D images. As shown in Fig. 8, ankerite precipitated around detrital quartz (large green area) and some small quartz inclusions in ankerite can be seen in 3D images.

The presence of calcite-filled veins indicates that fractures were opened and then sealed. Organic maturity of samples from Preese Hall-1 ranges from the oil window to the dry gas window (Clarke et al., 2018), and thus overpressuring could have occurred during hydrocarbon generation. The presence of overpressured fluids can result in the opening of

fractures and growth of calcite-filled veins (Marshall, 1982; Al-Aasm et al., 1993; Parnell et al., 1996; Dennis et al., 2019; Parnell et al., 2000). Moreover, some open fractures in samples from the Preese-Hall borehole could also have formed during tectonic periods (i.e., during the Variscan Orogeny) (Clarke et al., 2018).

Chlorite is present in the Bowland Shale and replaced calcite in some cases (Fig. 11e). It may have formed from the chloritization of kaolinite in the presence of carbonates at temperatures as low as 125 °C (Muffler and White, 1969). When present, bitumen-filled veins crosscut chlorite and calcite-filled veins. Bitumen in these veins was likely expelled during the renewed subsidence in the early Mesozoic as the maturity increases (Clarke et al., 2018).

## 5.2. Advantages of multi-scale and three dimensional methods in diagenetic studies

Despite significant developments in the understanding of diagenesis, it is often difficult to understand the relationships between minerals due to the limited information available from 2D images of sedimentary rocks. Table 2 shows the advantages of 3D imaging and how it differs from traditional SEM techniques. The formation order of quartz and carbonates is also difficult to unravel on the basis of 2D relationships. In previous studies, 2D images show that dolomite encloses quartz and feldspar cements (Bukar et al., 2021) as shown in Fig. 8a. However, based on different 2D slices and 3D images, carbonate can be seen to have precipitated within the framework provided by quartz. Nano-scale pores and pore systems in mudstones have been investigated using SEM
<figure><img src="image_12.png" /><figcaption>**Fig. 9.** Carbonates distribution and relationships in the Bowland Shale samples. (a) A 2D slice of zonation between non-ferroan dolomite (Z1), ferroan dolomite (Z3) and ankerite (Z2), sample B1, 2073.34 m. (b) The 3D reconstruction of non-ferroan dolomite. It shows a rhombic shape. (c) The 3D reconstruction of non-ferroan and its ferroan dolomite overgrowth. The outer surface of ferroan dolomite has some cavities. (d) The 3D reconstruction of non-ferroan dolomite and ankerite. Ankerite is partially in contact with non-ferroan dolomite. (e) The 3D reconstruction of zonation. It shows that ankerite is in contact with non-ferroan and ferroan dolomite. (f) A 2D slice of pore formed by the dissolution of ankerite, sample B1. (g) A 3D view of the pore within the ankerite. (h) A surface view of infilling the pore with organic matter (i.e. bitumen). (i) Pyrite in the pore, sample B4, 2089.83 m. (j) A surface view of organic matter infillings. Euhedral pyrite is present within the organic matter. NFD: non-ferroan dolomite; FD: ferroan dolomite; Ank: ankerite; Py: pyrite; OM: organic matter.</figcaption></figure>

images in previous studies and are commonly divided into organic matter-related and mineral-related pores (Loucks et al., 2012; Reed et al., 2020). With the development of X-ray tomography CT, the morphology of these pores can also be observed in 3D (Ma et al., 2016, 2017, 2018). This study has here identified carbonate dissolution pores, which can only be observed in 3D images. These carbonate dissolution pores differ from intra-mineral pores, which are located both within and outside of the mineral. They are larger than most of intra-mineral pores

and some of inter-mineral pores.

Zonation of carbonates can occur as a result of crystal growth (Paquette et al., 1993) and changes in fluid composition and/or redox, controlling differential incorporation of Fe (Jones, 2004; Denny et al., 2017). These models are well established but assume continuous crystal growth. In this study, the spatial interaction between non-ferroan dolomite, ferroan dolomite and ankerite shows that ankerite overgrew ferroan dolomite after partial ferroan dolomite dissolution, an
<figure><img src="image_13.png" /><figcaption>**Fig. 10.** Pores related to dolomite and ankerite. (a) Ankerite in sample B8. Intra- carbonate pores are few in sample B8, 2495.27 m. (b) Carbonates in sample B1, 2073.34 m. Dolomite and ankerite have a more clear outline than calcite. (c) Inter- mineral pores around carbonates in sample B1. (d) Intra- mineral pores within dolomite and ankerite in sample B1. Ank: ankerite; Cal: calcite; D: dolomite; Py: pyrite. (e) The intra- part of the carbonate dissolution pore. In this slice, the pore is present within the ankerite. (f) A 2D slice of the inter- mineral pore and carbonate dissolution pore. (g) The inter- part of the carbonate dissolution pore. In this slice, the same pore is present outside the ankerite. (h) A 2D slice of intra- mineral pore within the ankerite. (i) 3D reconstruction of a carbonate mineral and three types of pores. Orange line represents the slice shown in Fig. 10e. Blue line represents the slice shown in Fig. 10f. Black arrow means that the slice moved towards to the sample top. The carbonate dissolution pore is shown in yellow box. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)</figcaption></figure>

observation revealed by 3D data. This suggests a break in mineral precipitation between dolomite and ankerite. In previous studies, Hendry et al. (2000) interpreted zonation of ankerite and dolomite as ferroan dolomite overgrowths on previously formed ankerite. Bojanowski (2014) attributed the zonation to the precipitation of ankerite in the cavities between two phases of dolomite, which were formed by the dissolution of dolomite. Ma et al. (2021b) estimated that the precipitation temperature of dolomite-ankerite zonation ranges from 80 to 160 °C, with a sign of carbonate dissolution in the corroded areas. In this study, Figs. 9f-h show that in 3D evidence for carbonate dissolution and

infilling by bitumen in dissolved space. This suggests that the dissolution of ferroan dolomite is likely related to organic acid (Mazzullo and Harris, 1992; Pearce et al., 2018). Moreover, Fe-rich carbonates can also dissolve when they react with CO₂ and have a high reactivity with the presence of both CO₂ and SO₂ (Bertier et al., 2006; Weibel et al., 2014; Pearce et al., 2015). CO₂ might have been introduced into the brine during organic matter maturation in the oil window in this study. However, for key features such as quartz overgrowth and some clay minerals (i.e., illite and illite/smectite mixed-layer clay minerals), they cannot be easily identified in 3D images. Hence, the combination of 2D
<figure><img src="image_14.png" /><figcaption>**Fig. 11.** Calcite in the Bowland Shale samples. (a) The replacement of albite by late calcite cements, sample B5, 2091.69 m. (b) Pores within the calcite, sample B5. (c) Calcite-filled veins crosscutting quartz-rich bands, sample B8, 2495.27 m. (d) Dull orange cathodoluminescence of calcite-filled veins, sample B8. (e) The replacement of calcite cements in veins by chlorite, sample B8. (f) Bitumen-filled veins crosscutting calcite-filled veins and chlorite, sample B8. Qz: quartz; Alb: albite; Cal: calcite; Chl: chlorite. D: dolomite; FD: ferroan dolomite.</figcaption></figure>

and 3D images is a valuable way to study the mineral development in mudstones, sandstones and carbonate rocks.

### 5.3. Implications for carbon storage

The Bowland Shale from the Preese Hall-1 borehole, due to its low matrix permeability ($<1.5 \times 10^{-5} \text{ mD}$) (Clarke et al., 2018), is typical of caprocks that might be in place above carbon storage reservoirs. Leakage of CO₂ can occur through diffusive loss, flow through pore spaces, flow through fractures or well leakage (Song and Zhang, 2013). The Bowland Shale samples are generally unlaminated or interlaminated (Fauchille et al., 2017) without abundant fractures, therefore the risk of direct leakage through open fractures is negligible. The

presence of dissolved CO₂ in brine causes mineralogical changes in deep buried mudstones, resulting in changes in carbonates and clay minerals (Kaszuba et al., 2005; Credoz et al., 2009). Some minerals that are sensitive to CO₂-brine mixed fluid, including albite, calcite, dolomite, chlorite and kaolinite, are present in the Bowland Shale samples (Gaus, 2010; Jayasekara et al., 2020). The presence of carbonate dissolution pores is an indication of how pores might be formed after the reaction with CO₂. Their presence indicates a dissolution of carbonate from the outer surface inwards. Calcite-filled veins and dolomite cement may also dissolve during interaction with CO₂-loaded fluid, leading to new flow pathways with leakage risks (Kolawole et al., 2022). According to the paragenetic sequence in this study, the dissolution of carbonates was followed by the precipitation of ankerite. It has been proposed that the
<figure><img src="image_15.png" /><figcaption>Fig. 12. Interpreted paragenetic sequence of diagenesis in Bowland Shale samples. There are two phases of calcite cements.</figcaption></figure>

<table><caption>**Table 2**
The comparison of observations in 2D and 3D images.</caption><thead><tr><th>Minerals</th><th>2D observations</th><th>3D observations</th></tr></thead><tbody><tr><td>Pyrite</td><td>1. The shape and size of framboidal pyrite.<br>2. Their relationships with other minerals.</td><td>1. The morphologies of pyrite.<br>2. Inter- and intra-pores around pyrite, which can be quantified and measured.</td></tr><tr><td>Carbonates</td><td>1. The shape, size, distribution of carbonates.<br>2. Their relationships with surroundings (i.e., the replacement of calcite by chlorite).</td><td>1. Their spatial distribution and morphologies.<br>2. Relationships between different carbonate minerals. For example, zonation of dolomite, ferroan dolomite and ankerite.<br>3D images show that ferroan dolomite dissolved clearly.</td></tr><tr><td>Quartz</td><td>1. The shape, size and distribution of quartz.<br>2. Their relationships with surrounding minerals.<br>3. Quartz overgrowth. This can be observed in 2D images and hard to be discriminated in 3D images.</td><td>In 2D images, ankerite can be present around or adjacent to quartz. However, 3D images show that ankerite was precipitated within the space between quartz instead of surrounding quartz.</td></tr><tr><td>Pores</td><td>1. Pores can be observed in 2D images, which can be measured and quantified.<br>2. The identification of different types of pores.<br>3. Their distribution in samples.</td><td>1. Morphologies and connectivity of pores can be studied in 3D images.<br>2. 2D images are limited to identify different type of pores such as carbonate dissolution pores. This type of pores can be identified as inter- or intra-mineral pores in 2D images.<br>3. 3D images can provide the information about relationship between pores and minerals such as pyrite and organic dissolution pores. The identification and distribution of pores can help understand where minerals possibly precipitate during rock-fluid interactions.</td></tr></tbody></table>

dissolution of carbonate can be mitigated by the precipitation of new carbonate minerals (Wang et al., 2013). Ankerite occurs commonly as an overgrowth on the dolomite surface after the dissolution of ferroan

dolomite (Fig. 4a). Hence, it may precipitate in the dissolved areas. The bicarbonate produced by CO₂ injection can also incorporate Mg²⁺ or Fe²⁺ to form magnesite or siderite (Kaszuba and Janecky, 2009; Aminu et al., 2017). Ankerite and siderite are more stable than calcite and dolomite over a wide range of temperatures and pressures (Hendry, 2003). CO₂ could, therefore, eventually be permanently sequestered by precipitation of these magnesium and iron-bearing minerals (Johnson et al., 2004; Palandri and Kharaka, 2005).

As a large amount of CO₂ is injected in reservoirs, kaolinization of muscovite and albite may occur (Bjorkum and Gjelsvik, 1988; De Ros, 1998). Albite can dissolve in an acidic environment and release Al³⁺ that will react with soluble silica to form kaolinite. The increase in the volume of kaolinite has a negative relationship with the permeability and porosity of reservoirs as demonstrated experimentally (Mondol, 2009; Mondol et al., 2007). Quartz is also a product of the dissolution of feldspar after CO₂ injection (Gunter et al., 2000; Worden and Barclay, 2000). The precipitation of quartz or amorphous silica will occur as pH buffers towards neutral values (Kaszuba et al., 2005). Moreover, chlorite precipitation is a possible mechanism for trapping the CO₂ by quartz precipitation (Gaus, 2010). Hence, after the injection of CO₂, a large number of secondary pores or voids will be generated at first, followed by the precipitation of quartz, stable carbonate minerals and kaolinite. For the caprocks, during CO₂ injection dissolution occurs first but then kaolinite could precipitate, closing down permeability. This improves caprocks sealing capability and prevents leakage of CO₂ from the reservoirs.

## 6. Conclusions

1) The integration of 3D multi-scale X-ray tomography with standard 2D imaging provides a novel view to understand the mineral and pore micro textures in the Bowland Shale, and reveals its potential for applications to other subsurface storage systems.

2) 3D images provided much more detailed information about the relationships between quartz and ankerite, as well as the zonation of dolomite-ferroan dolomite-ankerite in this study, which cannot be clearly observed from 2D images.

3) Three types of carbonate-related pores were observed: intra-mineral pores, inter-mineral pores and carbonate dissolution pores. Specifically, carbonate dissolution pores can only be observed in 3D images
and their presence indicates a potential pathway for dolomite dissolution. Intra- and inter- mineral pores are also present within and around pyrite and micro-sized quartz, and the formation of these minerals likely helped resist compaction during diagenesis.

4) In some cases, 2D images show that ankerite was precipitated in the space around the quartz. However, in 3D images, their spatial relationship between quartz and ankerite shows that ankerite was precipitated within the space between quartz. 3D images also show that ankerite was formed after partial ferroan dolomite dissolution and then came into contact with dolomite, resulting in the dolomite-ferroan dolomite-ankerite zonation.

5) 3D images provide spatial information about dissolution pathways and features of carbonates, and thus help us better understand rock-fluid interactions after CO₂ storage. Ankerite, as a possible product after CO₂ storage, can precipitate in previously dissolved areas. The possible formation of kaolinite and quartz after CO₂ storage could also reduce the permeability of caprocks after mineral dissolution and improve the sealing capability of caprocks.

### CRediT authorship contribution statement

**Jingyue Hao:** Methodology, Investigation, Data curation, Writing – original draft. **Lin Ma:** Conceptualization, Methodology, Investigation, Writing – review & editing. **Cathy Hollis:** Supervision, Writing – review & editing. **Anne-Laure Fauchille:** Investigation, Writing – review & editing. **Kevin G. Taylor:** Supervision, Writing – review & editing.

### Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

### Data availability

Data will be made available on request.

### Acknowledgement

Dr. Tristan Lowe and Dr. Lewis Hughes are thanked for their technical assistance. Thanks for the support from the Diamond Light Source (I13-2 Diamond Manchester Imaging Branchline; MT15506-1) and National Research Facility for Lab X-ray CT (NXCT) through EPSRC grant EP/T02593X/1. JH would like to thank the China Scholarship Council for the PhD support (Ref 201806440002). LM wishes to acknowledge the fund from NERC fellowship (NE/R013527/1).

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