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Manuscript_9149fb37ed5a4eabaa98c3732b6ff193

1 X-ray computed tomography-based porosity analysis: Algorithms

2 and application for porous woody biomass

3 Quan Suna , Yidong Xia∗b , Jordan Klingerb , Robert Seifertb , Joshua Kanec , Vicki
4 Thompsonb and Qiushi Chen†a

a
5 The Glenn Department of Civil Engineering, Clemson University, Clemson, SC 29634, USA
b
6 Energy and Environment Science & Technology Directorate, Idaho National Laboratory, Idaho Falls, ID 83415,
7 USA
c
8 Materials and Fuels Complex, Idaho National Laboratory, Idaho Falls, ID 83415, USA

9 Abstract

10 The properties of lignocellulosic biomass, such as bulk physical, thermal, and mechanical prop-
11 erties, as well as the mobility of enzymes or catalysts, are largely affected by porosity, pore
12 structures, and pore size distribution. While X-ray computed tomography (CT) has been in-
13 troduced to effectively produce 3D volumetric images of material microstructure, a quantitative
14 porosity analysis from the 3D images has never been done. This work introduces a first-of-its-
15 kind X-ray CT-based quantitative porosity analysis method and applies the developed toolkit to
16 characterize the internal porosity distribution of loblolly pine. A sample loblolly pine chip was
17 scanned by a nano-resolution X-ray CT system and digitally reconstructed after a sequence of
18 image processing operations. A comprehensive porosity analysis was then performed to quan-
19 tify the envelope porosity, the spatial distribution of local porosity, and the directional porosity.
20 Solutions to the various challenges in image processing, porosity calculation, and large data
21 handling are provided.

22 Keywords: biomass feedstock; porosity; X-ray CT; image analysis; loblolly pine
∗
Co-corresponding author: Yidong Xia ([email protected])
†
Corresponding author: Qiushi Chen ([email protected])

1
© 2021 published by Elsevier. This manuscript is made available under the Elsevier user license
https://www.elsevier.com/open-access/userlicense/1.0/
23 1 Introduction

24 Porosity is a fundamental material property that effectively dictates the bulk physical, thermal,

25 and mechanical properties of lignocellulosic biomass [1]. The porosity, pore structure, and pore

26 size distribution of biomass directly affect the mobility of enzymes or catalysts for the extraction

27 of sugars and polysaccharides for the production of cellulosic ethanol [2]. For thermochemical

28 conversion to a biocrude intermediate, the porosity of biomass dictates the mass transport limitation

29 along with the particles, and the product quality as a result [3]. Porosity can impact the necessary

30 size reduction and preprocessing methods, and consequently, the cost of feedstock processing. For

31 the production of biomaterials, porosity can be critical for the application as a carbon amendment,

32 as activated carbon/charcoal, or as a polymer composite, among others.

33 While the definition of porosity, i.e., the ratio of the volume of voids over the total volume, is

34 straightforward, the accurate measurement and quantification of porosity is not. The traditional

35 approach to estimate the porosity of a material is the density method, where the porosity is com-

36 puted by comparing the bulk density of the material and the density of the solids in the dried

37 state. Although this method is widely used in the porosity determination of many materials such

38 as soils, rocks, and concrete, it may not be the most effective for biomass since the pore structure

39 of biomass is prone to break during the drying process [4]. In Brewer et al. [5], novel density mea-

40 surement techniques (i.e., the helium pycnometry and displacement of a dry granular suspension)

41 were developed to characterize the biochar density and porosity. For biomass, physisorption is

42 a more commonly used technique for porosity measurement. The term “physisorption” refers to

43 physical adsorption , a phenomenon of gas adhering to a material surface [6, 7]. Nitrogen has been

44 employed as the probe gas in cellulose research [8–11] for its stability and availability. Mercury

45 intrusion porosimetry (MIP) is another technique for quantifying pore structure and porosity. For

46 instance, Collet et al. [12] employed MIP to investigate the porous structure of hemp-based mate-

47 rials. In MIP, mercury is injected into the pore space by an imposed pressure, and porosity can be

48 estimated by correlating the volume of pores with the imposed pressure [13, 14].

49 Since the intrusion and adsorption media used in physisorption and MIP are sensitive to tem-

50 perature and air pressure, the fidelity of the porosity measurement is susceptible to the testing

51 environment. In comparison, imaging techniques provide distinct advantages and are a promising

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52 method for visualizing microstructures and quantifying porosity. Electron microscopes such as the

53 scanning electron microscope (SEM) and the transmission electron microscope (TEM) are often

54 used for porosity analysis. Early researchers such as White and Brown [15] visualized the hydrolysis

55 of cellulose using SEM. Their research provided a clear visualization of the degradation phenom-

56 ena at the nanoscale. Chundawat et al. [16] introduced TEM in multi-scale imaging of monocot

57 cell walls. Another pervasive method in biomass porosity analysis is nuclear magnetic resonance

58 (NMR). The pore size distribution of lignocellulosic substrate of the Populus was measured by

59 Meng et al. [17] using NMR, and they combined it with Simons’ stain method to probe the poros-

60 ity and assess the cellulose accessibility of biomass. Although these techniques have substantially

61 facilitated the development of porosity analysis, they have certain limitations. For example, the

62 sample preparation could affect the quality of the produced images [18], especially the introduction

63 of noise that may significantly disturb the results. More importantly, these techniques cannot pro-

64 vide three-dimensional (3D) information of pores, and thus the pore volumes must be estimated

65 indirectly.

66 X-ray computed tomography (CT) was introduced to effectively produce the 3D volumetric

67 images of material microstructures. Hamdi et al. [19] used X-ray CT for the morphological charac-

68 terization of lignocellulosic fiber and compared the X-ray CT image analysis results with those from

69 a commercial 2D document scanner. However, there was no analysis of the internal pore structure

70 or porosity. Ciesielski et al. [1] demonstrated visualizations of biomass particle geometry and mi-

71 crostructure using X-ray CT. Jones et al. [20] used X-ray CT to capture 3D images of biochar, but

72 their research concentrated on the pyrolysis of biochar. The bulk porosity is only used as a scalar in

73 the pyrolysis study. While the prior research used X-ray CT to analyze the properties of biomass,

74 there has been a lack of quantitative porosity analysis of biomass particles. This work fills the

75 gap by introducing a first-of-its-kind X-ray CT-based quantitative porosity analysis method and

76 applies the developed toolkit to characterize the internal porosity distribution of loblolly pine. A

77 sample of loblolly pine bark chip was scanned by a nano-resolution X-ray CT system and digitally

78 reconstructed after a sequence of image processing operations. A comprehensive porosity analysis

79 was then performed to measure the envelope porosity, the spatial distribution of local porosity, and

80 the directional porosity. Solutions to the various challenges in image processing, porosity analysis,

81 and large data handling are provided.

3
 82 2 Material and methods

83 The material studied is the debarked loblolly pine chips (Pinus taeda) harvested in South Carolina,

84 United States – a common type of forestry residual biomass in North America. A Phoenix v|tome|x

85 m nano-CT system (GE Sensing & Inspection Technologies GmbH, Wunstorf, Germany) with a peak

86 precision of sub-500 nanometers was used to scan the specimen.

87 2.1 Nano-CT imaging and processing

88 A diagram in Fig. 1 depicts the developed workflow of X-ray CT-based (or more specifically, nano-

89 resolution X-ray CT-based) digital reconstruction of 3D material microstructures. To set up a 3D

90 scan, a sample is fixed onto a holder in the system chamber and the holder is programmed to rotate

91 from 0◦ to 360◦ with an angular step size of 0.1◦ . Radiographs are collected at each angle. Using

92 GE’s proprietary software package phoenix datos|x, the projections are then reconstructed to a

93 3D volume. We then exported the raw grey-scale image slices from the software. For the pine chip,

94 a total of 3059 images were produced in an image stack. Each image is a slice along the Z-axis

95 and consists of 1934 (Y -direction) × 2174 (X-direction) pixels, and each pixel is 2 × 2 µm2 in size.

96 In the imaging stage, several resolution settings, from 0.5 µm to 4 µm were tested, and the 2 × 2

97 µm2 per pixel is the minimum value to preserve the fine voids in the pine chip. The storage size of

98 each image is about 8 MB, and the size of the entire image stack is 24.2 GB. One example image

99 of the raw CT image is shown in Fig. 1(b). A sequence of pre-processing operations for the raw

100 CT images was conducted using Fiji [21], an open-source image processing software toolkit that

101 supports scripted and command line operations. First, the threshold of the images was adjusted

102 based on the grey value histogram to distinguish the solid skeleton from the internal void space

103 and background. The proper range to identify the solid was manually determined by adjusting the

104 upper and lower bounds using the GUI of Fiji until a visually optimized result was reached. The

105 pixels showing the grayscale value within the selected range, from 51 to 208, were identified as solid

106 and binarized to a label value of 1. The rest of the pixels were identified as voids and set to 0 in its

107 label value. The binarization resulted in the black/white images of the particle (Fig. 1(c)). Then,

108 the salt-and-pepper noises, if they ever existed, were removed from every slice. One example of

109 the processed image from the stack is shown in Fig. 1(d). The size of the processed image stack

4
110 was reduced to 401 MB due to the binarization process. In the next step, the processed binary

111 image stack was converted to a 3D binary matrix, from which the 3D structure of the particle was

112 digitally reconstructed and visualized using MATLAB, shown in Fig. 1(e). The dimensions of the

113 chip specimen are 4,348 µm in length (X-direction), 3,868 µm in width (Y -direction), and 6,118 µm

114 in height (Z-direction). The digitally reconstructed pine chip is used as an example for quantitative

115 porosity analysis using algorithms developed and implemented in MATLAB, as detailed in the next

116 section.

117 2.2 Definitions of porosity

118 In this work, we distinguish and quantify three types of porosity regarding a pine chip: the envelope

119 porosity, local porosity (and its spatial distribution), and directional porosity. The definitions are

120 as follows.

121 • Envelope porosity: The envelope porosity (n), defined as the volume of the voids (Vv ) over

122 the envelope volume (V ∗ ) [22], is calculated using the following equation

Vv Nv
n= ∗
= ∗ (1)
V N

123 where Nv is the number of void voxels, N ∗ is the total number of voxels, and the superscript

124
∗ is used to indicate that the quantities are associated with the definition of the convex hull

125 enclosing the particle, as illustrated in Fig. 1(d). In this study, the MATLAB functions

126 regionprops3 and regionprops are employed to determine the convex hull of 3D and 2D

127 images, respectively.

128 • Local porosity: Fig. 2 illustrates how the local porosity is calculated. For any point location

129 inside a particle where the local porosity estimation is needed, we define a cubic volume of

130 select size, termed “kernel”. The center of the kernel coincides with the point location. The

131 local porosity for the point location is then calculated as the ratio of the number of void

132 voxels over the total number of voxels in the kernel. By moving the kernel one voxel at a time

133 over the envelope volume of the particle, the local porosity distribution of the particle can

134 be calculated. It should be noted that the selection of the kernel size, which is interpreted

5
135 by the edge length (Le ) of the cubic kernel, is problem-dependent and will be discussed in

136 detail in the next section. Also, compared with the envelope porosity calculation, the use of

137 a cubic kernel in the local porosity calculation indicates that local porosity in the vicinity

138 of the particle surface may be overestimated due to the existence of the marginal space, as

139 illustrated in Fig. 1(d).

140 • Directional porosity: the directional porosity describes the variation of local porosity along a

141 specified direction, e.g., along the X, Y , or Z direction. It is also a processed local porosity

142 to better demonstrate the heterogeneity of porosity. For example, Fig. 3 illustrates how

143 directional porosity is calculated along the Z direction. Each data point in the Z-directional

144 porosity profile corresponds to an averaged local porosity of the eroded convex hull. To avoid

145 the overestimation of porosity due to the surface marginal space, a convex hull is considered.

146 To ensure the entire kernel is within the convex hull, the convex hull is eroded by a half

147 kernel size. The local porosity values within the eroded convex hull are used to calculate the

148 averaged value.

149 2.3 Validation of the method

150 To assess and validate the fidelity of the developed method, a synthetic porous material was digitally

151 created, where the porosity can be calculated analytically. As shown in Fig. 4, the synthetic material

152 consists of 64 mono-sized spheres (with radius r), which are in their loosest packing state contained

153 in a cubic bounding box. The envelope porosity can be calculated analytically as:

Vsolid 64 × ( 34 π × r3 )
n=1− =1− = 0.4764 (2)
Vtotal 8r3

154 where Vsolid and Vtotal are the volume of the solid and total volume, respectively.

155 The developed method was applied to the 3D binary images of this synthetic material to calcu-

156 late the various porosities defined in Section 2.2. Since the 3D binary images have a finite resolution,

157 we first performed analysis to assess the sensitivity of the model-calculated envelope porosity to

158 the voxel resolution specified to the images. The loosest sphere packing can be regarded as aligned

159 arrays of spheres, and the analytical envelope porosity of such packing is equal to the porosity

6
160 of a cubic domain encompassing a single sphere, as shown in Fig. 5. The voxel resolution of the

161 3D binary images for a single sphere determines the accuracy of its spatial representation. For

162 instance, when the radius of the sphere is represented by 5 voxels, the resultant image of the sphere

163 looks serrated; when increasing to 100 voxels, the surface of the sphere becomes sufficiently smooth.

164 Higher voxel resolutions, however, will lead to higher computational costs. Fig. 6 shows the profile

165 of the calculated envelope porosity versus radius voxel number. As the number of voxels increases,

166 the calculated envelope porosity approaches the theoretical value of 0.4764. To make a balance

167 between the numerical accuracy and computational costs, we set the number of voxels (per radius

168 distance) to be 50 for the loose packing of 64 spheres, and accordingly, the edge length of the

169 bounding box of the loose packing is 400 voxels.

170 The developed method was then applied to the 3D synthetic binary image of the original loose

171 packing of 64 spheres. The calculated envelope porosity with a bounding box is 0.4767, closely

172 matching the theoretical value (0.4764). We also calculated the local porosity and directional

173 porosity of the loose packing using a kernel size of Le = 51 voxels. The results are visualized in

174 Fig. 7, where the distribution of the local porosity matches the packing of this synthetic material,

175 and the directional porosity shows a wave-like profile in each direction as expected for this packing.

176 3 Results and discussion

177 Using the scanned and digitally reconstructed pine chip, we present the porosity calculation results,

178 selection of kernel size, and the associated computational performance in this section.

179 3.1 Porosity calculations of the pine chip

180 The calculated envelope porosity, local porosity, and directional porosity of the pine chip are re-

181 ported as follows.

182 • Envelope porosity: the envelope porosity is 0.749 according to Eq. (1), which is within the

183 typical porosity range of 0.5 ∼ 0.8 for natural wood [23]. When the volume of a bounding

184 box (refer to Fig. 2) is used instead of the volume of the convex hull, the envelope porosity

185 is overestimated as 0.890 due to the inclusion of marginal space. This indicates that it is

186 essential to use the convex hull when processing complex-shaped objects.

7
187 • Local porosity: The fidelity of the local porosity depends on the specified kernel size. We

188 studied the impact of kernel size using seven edge lengths of the cubic kernel, Le : 6, 10,

189 14, 18, 30, 42, and 102 µm, respectively. Fig. 8 shows the local porosity distributions,

190 in which the color contours tend to be smoother with increasing kernel size, as expected.

191 Quantitatively speaking, larger kernel sizes resulted in smaller standard deviations of local

192 porosity distributions. For example, the range of local porosity in the case of Le = 102 µm

193 is much narrower than that in the case of Le = 6 µm. If the kernel is as large as nearly the

194 particle volume, the local porosity would be a single value close to the envelope porosity. On

195 the other hand, if the kernel size is equal to a voxel, i.e., Le = 2 µm, the local porosity value

196 would be either 0 or 1.

197 • Directional porosity: Fig. 9 shows the directional porosities along the X, Y , and Z directions

198 calculated with the seven kernel sizes. For all of the three directions, the profiles associated

199 with the kernel of Le = 102 µm (in brown color) yielded the lowest values, while those

200 associated with the kernel of Le = 6 µm (in dark blue color) yielded the highest values.

201 The differences between these profiles are, however, almost negligible, especially between

202 those with a kernel size smaller than Le = 102 µm. In addition, directional porosity is

203 a direct quantification of the heterogeneity of porosity along a given direction, while the

204 local porosity reflects the spatial distribution of porosity throughout the pine chip. The

205 shapes of the profiles are determined by how the solids (and voids) distribute along with

206 the corresponding directions. For the profiles in the X and Y directions, the prominent U

207 shape shows that there are fewer solids near the outer boundary of the chip than in the inner

208 region. It indicates that the local density of the pine chip is much higher in the central region

209 of the X-Y plane. We selected to compare two image slices from different locations in the

210 X-direction, as shown in Fig. 10. The first image slice contains only several solid voxels, and

211 therefore, the corresponding directional porosity value is almost equal to 1. As we move along

212 the X-direction, there are more solid voxels on each image slice. For example, on the 500th

213 image slice, the image contains many more solids, and therefore, has lower porosity values.

214 We also observed similar patterns in the Y -direction. On the contrary, there is an elevated

215 platform in the Z directional porosity curve, indicating a loose region (higher porosity) near

8
216 the center in the Z direction. The sharp jumps in the Z directional porosity curve also

217 indicate the apparent non-homogeneous microstructures in the pine chip, likely due to the

218 layered structures in wood. Fig. 11 shows four image slices selected at some key locations

219 on the Z-directional porosity curve. The sequence numbers for these four slices are 1, 150,

220 1100, and 1400, respectively (measured from the top of the pine chip). The first slice in the

221 Z-direction contains substantially more solid voxels compared to the first slices in the X- and

222 Y -directions. Thus, the starting point of the Z-directional porosity profile is lower than 1.

223 From the top edge to the central region, these images show the transition from looser solid

224 skeletons (e.g., 1st and 150th slices) to denser solid skeletons (e.g., 1100th slice) and back

225 to looser solid skeletons (e.g., 1400th slice), matching very well the observed fluctuations on

226 Z-directional porosity curve. In other words, the directional porosity curve can quantitatively

227 reflect the distribution of porosity (and solid skeleton) along a specified direction.

228 3.2 Recommendation of kernel size

229 To determine a proper kernel size for porosity analysis, we identified 444,845 voids in the 3D digital

230 reconstruction of the pine chip, with a histogram of their volumetric sizes plotted in Fig. 12. The

231 size of a void (consisting of connected void voxels) is defined as the major axis length of the void.

232 Only voids smaller than 30 µm are included in the histogram since more than 99.9% of the voids

233 are within this range. To characterize the inner voids in the porosity calculation, the kernel size

234 should be greater than the minimum void size to avoid “over-characterization”. For example, if

235 the size of a void is 30 voxels and a kernel with Le = 3 pixel resolution units is used, we will need

236 at least 10 kernels to encompass the void. This over-characterization would significantly increase

237 the computing time and data storage. On the other side, the kernel cannot be too large to lose

238 the essence of locality; the fine pore structures of the material analyzed need to be adequately

239 preserved. We recommend that a proper kernel size should be slightly larger than most of the

240 voids. In this study, a void size corresponding to 95% finer (by number) is 11.9 µm, meaning that

241 95% of the voids are finer than 11.9 µm. Among the seven kernel sizes investigated in Section 3.1,

242 the kernel size of 14 µm is recommended. We also investigated how kernel sizes affect the standard

243 deviation of local porosity values. As shown in Fig. 12, the standard deviation (σ) starts with a

244 high value (for smaller kernel size) and then decreases to a plateau as the kernel size increases.

9
245 The standard deviation fluctuates slightly around the plateau with the further increase of kernel

246 size. The recommended kernel size (Le = 14 µm) is at the transition to the plateau. Therefore, we

247 recommend that Le = 14 µm is a cost-accuracy balanced kernel size among the seven tested sizes

248 for the analyzed pine particle.

249 3.3 Computational performance

250 A primary challenge in the nano-resolution X-ray CT-based porosity analysis is how to overcome the

251 demanding requirement of computing time and data storage. For example, the 3D binary matrix

252 of the example pine particle consists of 1934 × 2174 × 3059 voxels. To traverse the entire volume

253 using a kernel of Le = 14 µm (i.e., 7 times of the 2 µm unit resolution), it requires 1.27 × 1010 times

254 of kernel computing, i.e., (1934 − 7) × (2174 − 7) × (3059 − 7) = 1.27 × 1010 .

255 To provide a reference for optimizing the computational performance, we investigated the in-

256 fluence of kernel size and the number of CPU cores with a 1000 µm3 sub-region cropped from the

257 entire volume. The same seven kernel sizes as used in Section 3.1 were tested. All computations

258 were conducted on the high-performance computing cluster Palmetto at Clemson University. The

259 requested computing nodes are DELL R740 with Intel Xeon 6148G Processors, and the code was

260 implemented in MATLAB. For each kernel size, the local porosity analyses were performed using 2,

261 8, 16, and 40 CPU cores, respectively. MATLAB utilizes multithreading automatically to exploit

262 natural parallelism. All simulations for the time profiling analysis were repeated twice to ensure

263 the results can be reproduced. Fig. 13 summarizes the computational costs for all tested cases. In

264 general, the increase of kernel size can result in a significant increase of computing time. For a

265 given kernel size, the increase in the number of CPU cores does not necessarily lead to a decrease

266 in computing time. The changes in the percentage of computing time are summarized in Table 1.

267 The computing time for N = 2 cases is used as the base for calculating the percentage change and

268 the values in the table are the average value of two repeated runs. Results in Table 1 show that

269 doubling the number of CPU core (meaning more energy consumption) leads to a reduction of time

270 much less than 50% – a strategy that is not necessarily cost-effective.

271 It is also worth noting that, to complete the local porosity analysis of the entire sample particle

272 using the kernel of 102 µm, it requires over 700 wall-clock hours with 40 CPU cores, far exceeding

273 the affordable time for such kind of analysis. One solution to reducing the wall-clock time is to

10
274 decompose the computational domain into sub-chunks and perform local porosity analysis on each

275 sub-chunk concurrently using parallel computing. Using this parallel scheme, we conducted a timing

276 test by decomposing the whole domain into 11 sub-chunks, assigning each sub-chunk to 40 CPU

277 cores, and running the analysis on 11 × 40 CPU cores concurrently. This effectively reduced the

278 wall-clock time to 67 hours. The local porosity distribution of the entire specimen can be obtained

279 by stitching the porosity analysis results of the sub-chunks. Improving computational efficiency

280 will be a continuous focus for analyses involving large imaging data.

281 4 Conclusions

282 In this study, we have presented a novel X-ray CT-based porosity analysis method and applied it

283 to study the micro-porosity of woody biomass. A loblolly pine particle was scanned by a nano-

284 resolution X-ray CT system and digitally reconstructed after a sequence of image processing op-

285 erations. Quantitative analyses on the particle envelope porosity, local porosity, and directional

286 porosity were conducted. The main conclusions are as follows. Firstly, the marginal space in a CT

287 image could lead to an overestimation of the envelope porosity; a rigorous specification and use

288 of a convex hull can effectively reduce the error. Secondly, the quantification of local porosity is

289 significantly influenced by the kernel size. An adequate kernel size should be slightly larger than

290 most of the voids to avoid over characterization but not too large to lose the essence of locality. In

291 this study, a kernel size of Le = 14 µm is recommended to characterize the local porosity, which

292 covers the top 95% void sizes. The directional porosity obtained by using Le = 14 µm illustrates

293 an anisotropic distribution of pores. The solids along the X and the Y direction concentrate near

294 the middle of the pine chip; while a loose section exists in the middle of the pine chip along the Z

295 direction. Thirdly, the kernel size and the number of CPU cores significantly impact the computa-

296 tional cost. In general, the increase of kernel size can result in a significant increase of computing

297 time. For a given kernel size, the increase in the number of CPU cores does not necessarily lead

298 to a decrease in computing time, which means simply doubling the number of CPU cores may

299 not be a cost-effective strategy. Future work will focus on the improvement of the computational

300 performance and the application of our analysis method to other biomass materials.

11
301 Acknowledgement

302 The research is primarily supported by the U.S. Department of Energy (DOE), Office of Energy

303 Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office (BETO), the Feedstock-

304 Conversion Interface Consortium (FCIC), under DOE Idaho Operations Office with Contract No.

305 DE-AC07-05ID14517. The research is also supported in part by DOE EERE under BETO award

306 no. DE-EE0008255.

307 Data availability

308 Source code and data related to this article will be hosted on an open-source online repository at

309 Github by the corresponding author (https://github.com/qschen/porosity-analysis.git).

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15
383 List of Figures
384 1 Nano-CT-based loblolly pine 3D microstructural topology reconstruction workflow:
385 (a) loblolly pine particles, (b) raw CT image slice, (c) binarized slice, (d) pre-
386 processed slice with convex hull, and (e) a digitally reconstructed particle in 3D.
387 The top row highlights methods used for each step. . . . . . . . . . . . . . . . . . . . 17
388 2 Schematic diagram of local porosity calculation. . . . . . . . . . . . . . . . . . . . . . 18
389 3 Schematic diagram of directional porosity calculation. . . . . . . . . . . . . . . . . . 19
390 4 A synthetic porous material consisting of 64 equal-sized loosely packed spheres in a
391 cubic bounding box. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
392 5 The effect of voxelized edge length. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
393 6 Envelope porosity against radius voxel number. . . . . . . . . . . . . . . . . . . . . . 22
394 7 Local porosity (upper left) and directional porosity of the loose packing (kernel size
395 Le = 51 voxels). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
396 8 Local porosity distribution at different kernel sizes (all subplots use the same color
397 bar). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
398 9 Directional porosity along X, Y and Z directions at different kernel sizes. . . . . . . 25
399 10 X-directional porosity and the 1st and 500th image slices. . . . . . . . . . . . . . . . 26
400 11 Z-directional porosity and the 1st, 150th, 1100th and 1400th image slices. . . . . . . 27
401 12 Histogram of void sizes (left) and the variation of standard deviation with kernel size
402 (right). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
403 13 Time cost of the 1000 µm3 subregion local porosity analysis, where N is the number
404 of CPU cores. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

16
 Nano-CT scan Binarization Median filtering 3D reconstruction
0, 0, 0, 0, 0, 0, 1, 1, 1
0 1 1 0 0 0
0 0 0 0 0 0
0 1 1 0 0 0 Example:
Solid range 0.4×0.4×0.8 mm3

Convex hull

Marginal space

6118𝜇𝑚
Z
Y
X
(a) (b) (c) (d) (e)
4348𝜇𝑚

Figure 1: Nano-CT-based loblolly pine 3D microstructural topology reconstruction workflow: (a) loblolly pine
particles, (b) raw CT image slice, (c) binarized slice, (d) pre-processed slice with convex hull, and (e) a digitally
reconstructed particle in 3D. The top row highlights methods used for each step.

17
 Kernel
void voxel

Z
local porosity at
Y kernel center
X solid voxel

Bounding box

Figure 2: Schematic diagram of local porosity calculation.

18
 Convex hull
Z Eroded convex hull

Marginal space

Average local porosity in

the eroded convex hull

0
1 ty
osi Dimensional porosity in Z direction
Por

Figure 3: Schematic diagram of directional porosity calculation.

19
Figure 4: A synthetic porous material consisting of 64 equal-sized loosely packed spheres in a cubic bounding box.

20
 Single sphere and its bounding box

r= 5 voxel 10 voxel 20 voxel 50 voxel 100 voxel

Figure 5: The effect of voxelized edge length.

21
 0.49

0.488

0.486

Porosity
0.484

0.482
Theoretical
0.48
value
0.478

0.476
5 10 20 50 100
Radius (Voxel number)

Figure 6: Envelope porosity against radius voxel number.

22
 1
Z-direction

0.8

0.6

0.4

0.2

0
0 50 100 150 200 250 300 350
Position (Voxel)

Figure 7: Local porosity (upper left) and directional porosity of the loose packing (kernel size Le = 51 voxels).

23
Figure 8: Local porosity distribution at different kernel sizes (all subplots use the same color bar).

24
Figure 9: Directional porosity along X, Y and Z directions at different kernel sizes.

25
 X‐direction

1st slice 500th slice

Zoom‐in view

Figure 10: X-directional porosity and the 1st and 500th image slices.

26
 Z‐direction

1th slice 150th slice 1100th slice 1400th slice

Zoom‐in
view

Figure 11: Z-directional porosity and the 1st, 150th, 1100th and 1400th image slices.

27
 Le = 14 µm
95% finer

Figure 12: Histogram of void sizes (left) and the variation of standard deviation with kernel size (right).

28
 Repeat 1 Repeat 2

N=2 N=2
104 104
N=8 N=8
N=16 N=16
N=40 N=40

103 103

6 10 14 18 30 42 102 6 10 14 18 30 42 102
Le ( m) Le ( m)

Figure 13: Time cost of the 1000 µm3 subregion local porosity analysis, where N is the number of CPU cores.

29
405 List of Tables
406 1 Percent change in computing time vs. kernel sizes for local porosity analysis. . . . . 31

30
Table 1: Percent change in computing time vs. kernel sizes for local porosity analysis.

Kernel size Number of CPU cores (N )

Le (µm) 2 8 16 40
6 100% +7.3% +9.2% -13.8%
10 100% +2.4% -5.7% -15.2%
14 100% +3.0% -9.4% -13.9%
18 100% +4.7% -4.8% -12.4%
30 100% +3.9% -8.0% -11.7%
42 100% +11.3% -1.1% -10.0%
102 100% -9.9% -22.6% -14.1%

31