This work was supported by funding from the Department of Radiology of the University of Bologna.

This protocol follows the guidelines of the institutional human research ethics committee.
1. Downloading the DICOM images
<ol>
	<li>Download the DICOM images and transfer them in the workstation dedicated to the segmentation, with the 3D software installed. If planning to work on a personal computer, anonymize the DICOM data.</li>
</ol>
2. Importing the HRCT study on the 3D Slicer software
<ol>
	<li>In the software opening screen (corresponding to the Welcome to Slicer section in the drop-down menu) select Load DICOM Data. Alternatively, select the DCM icon in the upper left corner of the toolbar.</li>
	<li>In the upper left corner of the DICOM Browser panel select Import, then select the location of the HRCT study. Select the folder with the DCM images, and then select Import.</li>
	<li>Now that the HRCT study has been successfully imported, click on the Load button.</li>
</ol>
3. Creating the Segments
<ol>
	<li>Create segments in the Segmentations section of the drop-down menu or directly in the sub-section Segment Editor found in the drop-down menu&#8217;s Segmentation section, or again as a dedicated icon in the toolbar.</li>
	<li>In the drop-down menu next to Master Volume, select the HRCT study.</li>
	<li>Select Add and create three new segments, which will be automatically named Segment 1, 2 and 3. Double click on each one and rename them respectively &#8220;tlv&#8221; (Total Lung Parenchyma), &#8220;ggo&#8221; (Ground Glass Opacities) and &#8220;cons&#8221; (Consolidations). If in the HRCT study additional pathological findings coexist, such as pleural effusion, lung cancer, fibrotic areas and so on, create additional segments. The same applies to artifacts.</li>
</ol>
4. Definition of the TLP segment
NOTE: An accurate definition of the TLP segment is fundamental, as it will be used for masking the HRCT during the definition of the GGO and CDs segments.
<ol>
	<li>As a first step, in the Segment Editor section, after selecting the TLP segment, choose the Threshold instrument.</li>
	<li>Set a threshold large enough to include both the healthy lung parenchyma and the ground glass opacities. Using the values reported in scientific literature with the necessary adjustments to comply with the textbook definition of GGO, we found that setting the threshold between -1000 HU and -250 HU works well6,14,15,16,17. Then select Apply.</li>
	<li>The segment so defined will include both the air inside the lungs and the air outside the chest (i.e., the air outside the patient). In order to isolate the lung parenchyma, use the Islands tool, found in the Segment Editor, and choose Keep selected island. Left click inside the chest so that anything outside the chest will be excluded from the segment.</li>
	<li>Next, include any area of consolidation inside the TLP segment. The consolidations usually have attenuation values (Hounsfield Units: HU) similar to those of soft tissues that constitute the chest wall and the mediastinum. This is the reason why the Threshold instrument cannot be used for this purpose and the consolidations will need to be added manually, using the Scissors and Paint tools found in the segment editor.
	<ol>
		<li>Use the Scissors tool to add portions of lung parenchyma to the segment. Choose the Fill Inside operation, select Free Form as the shape and Symmetric as the slice cut. Choose a thickness appropriate to the size of the consolidation (e.g., from 3 to 20 mm); and then, start progressively adding small portions of TLP, until the consolidation has been completely included.</li>
		<li>The Paint tool is easier and sometimes faster to use, but might be less precise, depending on the area to include. When the Sphere Brush option is active, this tool can add 3D portions of lung parenchyma to the segment. The size of the brush can be easily modified.</li>
		<li>While adding the consolidations to the TLP segment, do not include portions of thoracic wall or mediastinum. This could prove difficult as in patients affected by COVID19 consolidations adjacent to the posterior thoracic wall are quite common. Use the Erase tool to correct the segmentation or select Undo to discard the last action.</li>
		<li>At this stage, use the smoothing algorithm once more to delete small imperfections that might have occurred during the manual part of the segmentation. Now the TLP segment definition is concluded.</li>
	</ol>
	</li>
</ol>
5. Definition of the GGO segment
<ol>
	<li>To define the GGO segment, use the threshold tool.
	<ol>
		<li>Select the GGO segment.</li>
		<li>Set the threshold between -750 HU and -150 HU.</li>
		<li>Before selecting Apply, go to the Masking section right underneath and select TLP in the Editable Area drop down menu. In the Overwrite Other Segment drop-down menu, select None. This is extremely important as, if skipped, once defined the GGO segment, also the TLP segment would be modified. This must be avoided, as the TLP segment is the mask on which all the other segments are defined.</li>
		<li>Now select Apply.</li>
	</ol>
	</li>
	<li>At this point it will probably be necessary to use the smoothing algorithm once again, in order to exclude all the small vessels and the physiological interstitial elements that have a density similar to that of ground glass from the segment. Start with a Kernel size of 3 mm and, if needed, increase it progressively, to a maximum of 6-7 mm. Note that increasing the Kernel size too much might determine the loss of small areas of ground glass, which would be left outside the GGO segment. Because of this, the smoothing algorithm should be used with the proper caution.</li>
	<li>In this case too, apply needed corrections with the Paint, Scissors and Erase tool. During this phase remember to keep the TLP mask active at all times to avoid including portions of chest wall adjacent to the &#8220;ground glass&#8221; areas inside the segment. This is because, if erroneously segmented, they would automatically be excluded.</li>
	<li>When obtaining this segment, pay close attention to the possible presence of artifacts generated by movements of hearth and diaphragm (this happens if the patient could not hold his breath during the exam). If present and previously included in the TLP segment, eliminate these artifacts from the &#8220;ground glass&#8221; segment, for example through the Islands tool with the Remove Selected Island option or using the Scissors and Erase tools. Depending on the study&#8217;s goal, the artifacts might be segmented separately, using a dedicated segment or included in the TLP segment and excluded from other segments. Now the GGO segment has been defined.</li>
</ol>
6. Definition of the CDs segment
<ol>
	<li>To define the CDs segment, proceed the same way as to define the GGO segment.
	<ol>
		<li>Select the CDs segment. Be sure to work with the TLP masking always active.</li>
		<li>Set an adequate threshold. For consolidations the range varies, roughly, from -150 HU to 100 HU.</li>
		<li>Apply the smoothing algorithm varying the Kernel size as needed.</li>
		<li>Use a combination of the tools Scissors, Erase, Paint and Islands in order to keep inside the segment only the real consolidations, excluding large vessels, pleural effusions, artifacts, disventilatory bands and other non COVID-related lesions.</li>
		<li>If needed, apply a final smoothing might be applied.</li>
	</ol>
	</li>
</ol>
7. Saving the segments
<ol>
	<li>Save segments as an &#8220;.nrrd&#8221; file, or convert to binary label maps from the &#34;Data&#34; module.</li>
</ol>
8. Extracting volumes from the defined segments.
<ol>
	<li>From the Segment Statistics module, obtain a table with details on volume and surfaces of the segments.</li>
</ol>

<ol>
	<li>Zheng, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=COVID-19+and+the+cardiovascular+system.">COVID-19 and the cardiovascular system.</a> Nature Reviews Cardiology. 17, 259-260 (2020).</li><li>Simpson, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Radiological+Society+of+North+America+Expert+Consensus+Statement+on+Reporting+Chest+CT+Findings+Related+to+COVID-19.+Endorsed+by+the+Society+of+Thoracic+Radiology,+the+American+College+of+Radiology,+and+RSNA.">Radiological Society of North America Expert Consensus Statement on Reporting Chest CT Findings Related to COVID-19. Endorsed by the Society of Thoracic Radiology, the American College of Radiology, and RSNA.</a> Radiology: Cardiothoracic Imaging. 2, 2 (2020).</li><li>Xie, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chest+CT+for+Typical+2019-nCoV+Pneumonia:+Relationship+to+Negative+RT-PCR+Testing.">Chest CT for Typical 2019-nCoV Pneumonia: Relationship to Negative RT-PCR Testing.</a> Radiology. , 200343 (2020).</li><li>Huang, P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Use+of+Chest+CT+in+Combination+with+Negative+RT-PCR+Assay+for+the+2019+Novel+Coronavirus+but+High+Clinical+Suspicion.">Use of Chest CT in Combination with Negative RT-PCR Assay for the 2019 Novel Coronavirus but High Clinical Suspicion.</a> Radiology. 295 (1), 22-23 (2020).</li><li>Fang, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sensitivity+of+Chest+CT+for+COVID-19:+Comparison+to+RT-PCR.">Sensitivity of Chest CT for COVID-19: Comparison to RT-PCR.</a> Radiology. , 200432 (2020).</li><li>Colombi, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Well-aerated+Lung+on+Admitting+Chest+CT+to+Predict+Adverse+Outcome+in+COVID-19+Pneumonia.">Well-aerated Lung on Admitting Chest CT to Predict Adverse Outcome in COVID-19 Pneumonia.</a> Radiology. , 201433 (2020).</li><li>. 3D Slicer [software] Available from: <a target="_blank" href="https://www.slicer.org">https://www.slicer.org</a> (2020)</li><li>Kikinis, R., Pieper, S. D., Vosburgh, K., Jolesz, F. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=3D+Slicer:+a+platform+for+subject-specific+image+analysis,+visualization,+and+clinical+support.">3D Slicer: a platform for subject-specific image analysis, visualization, and clinical support.</a> Intraoperative Imaging Image-Guided Therapy. 3 (19), 277-289 (2014).</li><li>Kapur, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Increasing+the+impact+of+medical+image+computing+using+community-based+open-access+hackathons:+The+NA-MIC+and+3D+Slicer+experience.">Increasing the impact of medical image computing using community-based open-access hackathons: The NA-MIC and 3D Slicer experience.</a> Medical Image Analysis. 33, 176-180 (2016).</li><li>Fedorov, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=3D+Slicer+as+an+Image+Computing+Platform+for+the+Quantitative+Imaging+Network.">3D Slicer as an Image Computing Platform for the Quantitative Imaging Network.</a> Magnetic Resonance Imaging. 30 (9), 1323-1341 (2012).</li><li>. Chest Imaging Platform [software] Available from: <a target="_blank" href="https://chestimagingplatform.org">https://chestimagingplatform.org</a> (2020)</li><li>Wang, J., Li, F., Li, Q. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Automated+segmentation+of+lungs+with+severe+interstitial+lung+disease+in+CT.">Automated segmentation of lungs with severe interstitial lung disease in CT.</a> Medical Physics. 36 (10), 4592-4599 (2009).</li><li>Lanza, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+chest+CT+analysis+in+COVID-19+to+predict+the+need+for+oxygenation+support+and+intubation.">Quantitative chest CT analysis in COVID-19 to predict the need for oxygenation support and intubation.</a> European Radiology. , (2020).</li><li>Yao, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Value+of+window+technique+in+diagnosis+of+the+ground+glass+opacities+in+patients+with+non-small+cell+pulmonary+cancer.">Value of window technique in diagnosis of the ground glass opacities in patients with non-small cell pulmonary cancer.</a> Oncology Letters. 12 (5), 3933-3935 (2016).</li><li>Kauczor, H. U., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Automatic+detection+and+quantification+of+ground-glass+opacities+on+high-resolution+CT+using+multiple+neural+networks:+comparison+with+a+density+mask.">Automatic detection and quantification of ground-glass opacities on high-resolution CT using multiple neural networks: comparison with a density mask.</a> American Journal of Roentgenology. 175 (5), 1329-1334 (2000).</li><li>Funama, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Detection+of+nodules+showing+ground-glass+opacity+in+the+lungs+at+low-dose+multidetector+computed+tomography:+phantom+and+clinical+study.">Detection of nodules showing ground-glass opacity in the lungs at low-dose multidetector computed tomography: phantom and clinical study.</a> Journal of Computed Assisted Tomography. 33 (1), 49-53 (2009).</li><li>Hansell, D. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fleischner+Society:+glossary+of+terms+for+thoracic+imaging.">Fleischner Society: glossary of terms for thoracic imaging.</a> Radiology. 246, 697-722 (2008).</li><li>Heye, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reproducibility+of+Dynamic+Part+II.+Comparison+of+Intra-+and+Interobserver+Variability+with+Manual+Region+of+Interest+Placement+versus+semiautomatic+lesion+segmentation+and+histogram+analysis.">Reproducibility of Dynamic Part II. Comparison of Intra- and Interobserver Variability with Manual Region of Interest Placement versus semiautomatic lesion segmentation and histogram analysis.</a> Radiology. 266, 812-821 (2013).</li><li>Zhang, H. T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Automated+detection+and+quantification+of+COVID-19+pneumonia:+CT+imaging+analysis+by+a+deep+learning-based+software.">Automated detection and quantification of COVID-19 pneumonia: CT imaging analysis by a deep learning-based software.</a> Nuclear Medicine and Molecular Imaging. 14, 1-8 (2020).</li><li>Alhazzani, W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Surviving+Sepsis+Campaign:+guidelines+on+the+management+of+critically+ill+adults+with+Coronavirus+Disease+2019(COVID-19).">Surviving Sepsis Campaign: guidelines on the management of critically ill adults with Coronavirus Disease 2019(COVID-19).</a> Intensive Care Medicine. 46 (5), 854-887 (2020).</li></ol>

None of the authors have conflicts of interests.

Segmentation represents a fundamental step for performing modern quantitative radiology studies, and is necessary to apply radiomics or texture analysis techniques. Pathological findings in the lungs represent one of the most challenging to segment, for the lack of defined anatomical borders and a small difference in attenuation value when compared to the healthy areas.
The source images must present with a minimum of artifacts if possible, especially on the pathological areas, and this is sometimes hard to achieve when studying a disease that compromises breath holding; therefore, researchers can consider excluding compromised HRCTs or defining a segment dedicated to artifacts to be eliminated from further analysis.
It is possible to install an extension to 3D Slicer, called the &#8220;chest imaging platform&#8221;11, which allows faster, more automated operations on lung segments, with particular interest on aerated lung. It was decided not to adopt this method, since it requires extensive manual intervention when GGO and consolidations have a sub-pleural distribution, which is the case of the pathology explored in this paper.
An automatic segmentation method for interstitial lung diseases has been reported12; even so, this method required having previous knowledge of the affected areas&#8217; features. The technique proposed in this study represents an easy to learn and reproducible approach to segmentation of pathological findings of the lung, the features extracted from which could provide future means of automatically segment viral interstitial lung diseases, and represent accurate prognostic factors.
The segmentation method proposed has some limitations.
First of all, downloading the DICOM images from the workstations is a process that might require a variable amount of time, thus doing so for vast numbers of patients might be a troublesome work. Any potential application of this segmentation method to the clinic practice must consider this critical issue, until the point when segmentation plugins become widely available on PACS platforms.
Secondly, the segmentation of the COVID-19 related pathological areas might be complicated in patients with concurrent chronic lung disease (e.g., lung cancer, lung fibrosis, etc.) whose radiological findings consist in areas with the same densities of those typical of COVID-19 patterns. The same concern should be considered in CT scans with respiratory artifacts. These artifacts are quite common in patients with COVID-19 infection, being commonly related to dyspnea and respiratory failure, especially in old/middle aged patients.
Moreover, patients with a severe interstitial pneumonia (characterized by many lung consolidations and crazy paving opacities) require a more extensive manual segmentation and consequently, a vast amount of time. In general, the higher the severity of the interstitial pneumonia, the more extensive the manual segmentation required, the longer the segmentation time.
However, the degree of precision offered by advanced evaluation techniques such as the ones proposed by Lanza and Colombi could add limited information on patients with already severe lung conditions compared to the standard clinical and radiological evaluations20.
Finally, it should be noted that any radiologist who has no experience with 3D slicer needs an adequate training time, as it is not an intuitive software and requires some time to be mastered even in its basilar functions.

In the current year, the world is facing a health emergency, the pandemic caused by the novel Coronavirus, Sars-CoV2. Even if, up to the present date, many aspects regarding the physiopathology of the COVID-19 infection are still unclear, it shares several characteristics with its &#8220;ancestors&#8221; SARS1 and MERS. In particular, it has been proven that the virion spike proteins interact with the Angiotensin Converting Enzyme Type-2, a receptor well represented on the alveolar endothelial cells, but ubiquitous in the human organism, thus having the potentiality to give systemic symptoms1.
For diagnosis, the current standard is the real-time reverse transcriptase-polymerase chain reaction (rt-PCR), a test performed on pharyngeal swabs. Although radiological imaging is not officially recognized in the diagnostic path for the detection of the disease, high resolution computed tomography (HRCT) proved to be a valuable aid to the clinical and epidemiological management of affected patients, due to the relatively low sensitivity of the rt-PCR, the current scarcity of specialized laboratories and of the necessary reagents, and the high operator-dependency.
The Radiological Society of North America (RSNA) released a consensus statement, endorsed by the society of Thoracic Radiology and the American College of Radiology (ACR), that classifies the CT appearance of COVID19 into four categories in order to standardize the reporting, dividing the interstitial pneumonia patterns into &#8220;typical&#8221;, &#8220;atypical&#8221;, &#8220;indetermined&#8221;, and &#8220;negative&#8221;2.
The &#8220;typical&#8221; pattern is characterized by the presence of round-shaped Ground Glass Opacities (GGO), usually with a sub-pleural location on the dorsal basal segments. The GGO can be associated with &#8220;Crazy Paving&#8221; areas of thickened septa, or other signs of organizing pneumonia. The &#8220;indetermined&#8221; pattern is characterized by the absence of the &#8220;typical&#8221; pattern findings, with diffuse GGO areas with a perihilar distribution, with or without consolidative areas. The &#8220;atypical&#8221; pattern is characterized by either the absence of the &#8220;typical&#8221; or &#8220;undetermined&#8221; signs, and the presence of lobar consolidations, &#8220;tree in bud&#8221;, smooth thickening of the septa and pleural effusion; in this presentation no GGO are detectable. The &#8220;negative&#8221; pattern is characterized by the absence of the aforementioned pathological findings.
According to literature, some patients may present with a high clinical suspect of COVID-19 supported by epidemiological criteria and imaging finding with negative rt-PCR3,4. On the other hand, it has been reported that patients with a positive rt-PCR and suggestive clinical findings, do not present pathological findings on HRCT5.
Nowadays, it is of paramount interest for the scientific community to apply image analysis techniques when quantitatively studying the characteristics of this disease. A recent study has applied automated segmentation technique of the lung parenchyma to identify the percentage of aerated lung in patients affected by COVID-19, correlating this value with the prognosis, and demonstrating that patients with a more severe lung involvement presented more risk of being admitted in the Intensive Care Unit (ICU), and having worse outcomes6.
The segmentation is the contouring of regions of interest (ROIs) inside a volume acquired through an imaging technique, such as HRCT. This activity may be carried out though three methods: manual, semi-automatic and automatic. Manual segmentation, thanks to the experience of a trained radiologist, consists of labelling voxels belonging to the pathological area. The main disadvantages of this method are the large amount of time required and the fact that it is operator-dependent.
Semi-automatic methods allow to speed up the segmentation as the operator can modify a segmentation mask obtained through the classic methods of image processing (e.g., threshold on pixel intensity, clustering, etc.). However, these techniques are not easy to implement in clinical practice as they require extensive manual intervention in the most complicated cases18.
Automatic segmentation methods, currently of limited use, employ artificial intelligence to obtain ROIs. In particular, a recent study aims to use automatic segmentation in the quantification of ground glass areas in patients suffering from COVID-19 interstitial pneumonia19. The definition of a segmentation protocol for the pathological areas on the HRCT images is the real first step toward the subsequent radiomics analysis, in order to identify features that could help to further understand the physiopathology of the disease, and serve as an accurate prognostic factor potentially influencing the treatment.
This paper offers a guide to obtain accurate and efficient segments representing the pathological findings of COVID-19 pneumonia using &#8220;3D Slicer&#8221;7,8,9,10.

<table><tbody><tr><td>CT Scanner</td><td>General Electrics Healthcare</td><td>64-MDCT VCT lightSpeed</td><td>The CT scanner used for HRCT acquisitions</td></tr><tr><td>Desktop Computer</td><td>ThinkCentre</td><td></td><td>The computer used to download the DICOM files and run 3D Slicer</td></tr></tbody></table>

lung ct segmentation to identify consolidations and ground glass areas for quantitative assesment of sars-cov pneumonia

Segmentation is a complex task, faced by radiologists and researchers as radiomics and machine learning grow in potentiality. The process can either be automatic, semi-automatic, or manual, the first often not being sufficiently precise or easily reproducible, and the last being excessively time consuming when involving large districts with high-resolution acquisitions.
A high-resolution CT of the chest is composed of hundreds of images, and this makes the manual approach excessively time consuming. Furthermore, the parenchymal alterations require an expert evaluation to be discerned from the normal appearance; thus, a semi-automatic approach to the segmentation process is, to the best of our knowledge, the most suitable when segmenting pneumonias, especially when their features are still unknown.
For the studies conducted in our institute on the imaging of COVID-19, we adopted 3D Slicer, a freeware software produced by the Harvard University, and combined the threshold with the paint brush instruments to achieve fast and precise segmentation of aerated lung, ground glass opacities, and consolidations. When facing complex cases, this method still requires a considerable amount of time for proper manual adjustments, but provides an extremely efficient mean to define segments to use for further analysis, such as the calculation of the percentage of the affected lung parenchyma or texture analysis of the ground glass areas.

The proposed method has been refined through trials and errors, testing it on 117 patients affected by COVID-19 pneumonia with a positive rt-PCR test.
After a short learning curve, the time needed to obtain the segments can vary from 5 to 15 minutes, depending on the presentation pattern.
As shown on Figure 1, the method yields precise segments: this can be observed by noticing the exact correspondence with the HRCT. The 3D rendering helps to assess the correspondence and quickly review the segmentation results. A quantitative assessment of the amount of lung parenchyma affected can be obtained, to replicate the results reported from Colombi et al.6 and Lanza et al.13.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/61737/61737fig1.jpg" /> 
Figure 1: Representative results volume and surface analysis. The screenshot from the 3D Slicer interface represents the results obtained from the &#8220;Segment Statistics&#8221; module, which can be used to quantitatively evaluate the volume of the affected lung parenchyma. <a href="https://www-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/61737/61737fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about Lung CT Segmentation to Identify Consolidations and Ground Glass Areas for Quantitative Assesment of SARS-CoV Pneumonia at JoVE.com

Lung CT Segmentation to Identify Consolidations and Ground Glass Areas for Quantitative Assesment of SARS-CoV Pneumonia

The aim of this protocol is to provide a time efficient way to segment volumes of interest on high-resolution CT scans to use for further radiomics analysis.

Segmentation is a complex task, faced by radiologists and researchers as radiomics and machine learning grow in potentiality. The process can either be ...

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14.1K Views.  University of Bologna. The aim of this protocol is to provide a time efficient way to segment volumes of interest on high-resolution CT scans to use for further radiomics analysis.

Video: Lung CT Segmentation to Identify Consolidations and Ground Glass Areas for Quantitative Assesment of SARS-CoV Pneumonia

Analysis of 18FDG PET/CT Imaging as a Tool for Studying Mycobacterium tuberculosis Infection and Treatment in Non-human Primates

Mycobacterium tuberculosis remains the number one infectious agent in the world today. With the emergence of antibiotic resistant strains, new clinically relevant methods are needed that evaluate the disease process and screen for potential antibiotic and vaccine treatments. Positron Emission Tomography/Computed Tomography (PET/CT) has been established as a valuable tool for studying a number of afflictions such as cancer, Alzheimer&#39;s disease, and inflammation/infection. Outlined here are a number of strategies that have been employed to evaluate PET/CT images in cynomolgus macaques that are infected intrabronchially with low doses of M. tuberculosis. Through evaluation of lesion size on CT and uptake of 18F-fluorodeoxyglucose (FDG) in lesions and lymph nodes in PET images, these described methods show that PET/CT imaging can predict future development of active versus latent disease and the propensity for reactivation from a latent state of infection. Additionally, by analyzing the overall level of lung inflammation, these methods determine antibiotic efficacy of drugs against M. tuberculosis in the most clinically relevant existing animal model. These image analysis methods are some of the most powerful tools in the arsenal against this disease as not only can they evaluate a number of characteristics of infection and drug treatment, but they are also directly translatable to a clinical setting for use in human studies.

Analysis of 18FDG PET/CT Imaging as a Tool for Studying Mycobacterium tuberculosis Infection and Treatment in Non-human Primates

Here, we present a protocol to describe the analysis of 18F-FDG PET/CT imaging in non-human primates that have been infected with M. tuberculosis to study disease process, drug treatment, and disease reactivation.

Mycobacterium tuberculosis remains the number one infectious agent in the world today. With the emergence of antibiotic resistant strains, new clinically ...

Immunology and Infection

Protocol and Guidelines for Point-of-Care Lung Ultrasound in Diagnosing Neonatal Pulmonary Diseases Based on International Expert Consensus

Ultrasound is a safe bedside imaging tool that obviates the use of ionizing radiation diagnostic procedures. Due to its convenience, the lung ultrasound has received increasing attention from neonatal physicians. Nevertheless, clear reference standards and guideline limits are needed for accurate application of this diagnostic modality. This document aims to summarize expert opinions and to provide precise guidance to help facilitate the use of the lung ultrasound in the diagnosis of neonatal lung diseases.

Lung ultrasound is a noninvasive and valuable tool for bedside evaluation of neonatal lung diseases. However, a relative lack of reference standards, protocols and guidelines may limit its application. Here, we aim to develop a standardized neonatal lung ultrasound diagnostic protocol to be used in clinical decision-making.

Ultrasound is a safe bedside imaging tool that obviates the use of ionizing radiation diagnostic procedures. Due to its convenience, the lung ultrasound ...

Imaging Features of Systemic Sclerosis-Associated Interstitial Lung Disease

Early diagnosis of systemic sclerosis-related interstitial lung disease (SSc-ILD) is important to enable treatment to be administered with minimal delay. However, diagnosing SSc-ILD is challenging because key symptoms are non-specific. High-resolution computed tomography (HRCT) of the chest is recognized as a sensitive imaging method for diagnosing and assessing SSc-ILD. Exposure of patients to ionizing radiation may be considered as a limitation, although methodological steps may be taken to moderate this. We present practical recommendations for performing HRCT scans and interpreting the results. Key features of SSc-ILD on HRCT include a non-specific interstitial pneumonia (NSIP) pattern with peripheral ground-glass opacities and extensive traction bronchiectasis. Despite similarities between SSc-ILD and idiopathic pulmonary fibrosis (IPF), HRCT can be used to differentiate between these conditions: in SSc-ILD compared with IPF, there is a greater proportion of ground-glass opacity and fibrosis is less coarse. A dilated, air-filled esophagus with diameter &#62;10 mm, suggestive of esophageal dysmotility is commonly seen in SSc-ILD. Pulmonary artery size greater than the adjacent ascending aorta suggests coexistent pulmonary hypertension. Nodules must be monitored due to the increased risk of lung cancer. A large extent of disease on HRCT (&#8805;20%) or a high fibrosis score suggests an increased risk of mortality. HRCT is central to diagnosing SSc-ILD, and serial assessments can be helpful in monitoring disease progression or treatment response.

Here, we present practical recommendations for performing thoracic high-resolution computed tomography for diagnosing and assessing systemic sclerosis-related interstitial lung disease.

Early diagnosis of systemic sclerosis-related interstitial lung disease (SSc-ILD) is important to enable treatment to be administered with minimal delay. ...

DUCT: Double Resin Casting followed by Micro-Computed Tomography for 3D Liver Analysis

The liver is the biggest internal organ in humans and mice, and high auto-fluorescence presents a significant challenge for assessing the three-dimensional (3D) architecture of the organ at the whole-organ level. Liver architecture is characterized by multiple branching lumenized structures, which can be filled with resin, including vascular and biliary trees, establishing a highly stereotyped pattern in the otherwise hepatocyte-rich parenchyma. This protocol describes the pipeline for performing double resin casting micro-computed tomography, or &#34;DUCT&#34;. DUCT entails injecting the portal vein and common bile duct with two different radiopaque synthetic resins, followed by tissue fixation. Quality control by clearing one lobe, or the entire liver, with an optical clearing agent, allows for pre-screening of suitably injected samples. In the second part of the DUCT pipeline, a lobe or the whole liver can be used for micro-computed tomography (microCT) scanning, (semi-)automated segmentation, and 3D rendering of the portal venous and biliary networks. MicroCT results in 3D coordinate data for the two resins allowing for qualitative as well as quantitative analysis of the two systems and their spatial relationship. DUCT can be applied to postnatal and adult mouse liver and can be further extended to other tubular networks, for example, vascular networks and airways in the lungs.

Double resin casting micro-computed tomography, or DUCT, enables visualization, digitalization, and segmentation of two tubular systems simultaneously to facilitate 3D analysis of organ architecture. DUCT combines ex vivo injection of two radiopaque resins followed by micro-computed tomography scanning and segmentation of the tomographic data.

The liver is the biggest internal organ in humans and mice, and high auto-fluorescence presents a significant challenge for assessing the ...

Point-of-Care Lung Ultrasound in Adults: Image Acquisition

Consultative ultrasound performed by radiologists has traditionally not been used for imaging the lungs, as the lungs&#39; air-filled nature normally prevents direct visualization of the lung parenchyma. When showing the lung parenchyma, ultrasound typically generates a number of non-anatomic artifacts. However, over the past several decades, these artifacts have been studied by diagnostic point-of-care ultrasound (POCUS) practitioners, who have identified findings that have value in narrowing the differential diagnoses of cardiopulmonary dysfunction. For instance, in patients presenting with dyspnea, lung POCUS is superior to chest radiography (CXR) for the diagnosis of pneumothorax, pulmonary edema, lung consolidations, and pleural effusions. Despite its known diagnostic value, the utilization of lung POCUS in clinical medicine remains variable, in part because training in this modality across hospitals remains inconsistent. To address this educational gap, this narrative review describes lung POCUS image acquisition in adults, including patient positioning, transducer selection, probe placement, acquisition sequence, and image optimization.

Point-of-care ultrasound (POCUS) of the lungs provides quick answers in rapidly changing clinical scenarios. We present an efficient and informative protocol for image acquisition for use in acute care settings.

Consultative ultrasound performed by radiologists has traditionally not been used for imaging the lungs, as the lungs&#39; air-filled nature normally ...

Enhancing Pulmonary Nodule Diagnosis Using Whole-Lung 3D Reconstruction

Three-Dimensional Reconstruction for the Whole Lung with Early Multiple Pulmonary Nodules

For patients with early multiple pulmonary nodules, it is essential, from a diagnostic perspective, to determine the spatial distribution, size, location, and relationship with surrounding lung tissue of these nodules throughout the entire lung. This is crucial for identifying the primary lesion and developing more scientifically grounded treatment plans for doctors. However, pattern recognition methods based on machine vision are susceptible to false positives and false negatives and, therefore, cannot fully meet clinical demands in this regard. Visualization methods based on maximum intensity projection (MIP) can better illustrate local and individual pulmonary nodules but lack a macroscopic and holistic description of the distribution and spatial features of multiple pulmonary nodules.
Therefore, this study proposes a whole-lung 3D reconstruction method. It extracts the 3D contour of the lung using medical image processing technology against the background of the entire lung and performs 3D reconstruction of the lung, pulmonary artery, and multiple pulmonary nodules in 3D space. This method can comprehensively depict the spatial distribution and radiological features of multiple nodules throughout the entire lung, providing a simple and convenient means of evaluating the diagnosis and prognosis of multiple pulmonary nodules.

Author Spotlight: Advancing 3D Modeling for Enhanced Diagnosis and Treatment of Pulmonary Nodules in Early-Stage Lung Cancer 

This study introduces a three-dimensional (3D) reconstruction method for the entire lung in patients with early multiple pulmonary nodules. It offers a comprehensive visualization of nodule distribution and their interplay with lung tissue, simplifying the assessment of diagnosis and prognosis for these patients.

For patients with early multiple pulmonary nodules, it is essential, from a diagnostic perspective, to determine the spatial distribution, size, location, ...

Multi-modal Pulmonary Imaging: Using Complementary Information from CT and Hyperpolarized 129Xe MRI to Evaluate Lung Structure-Function

Hyperpolarized 129Xe gas MRI is an emerging technique to evaluate and measure regional lung function including pulmonary gas distribution and gas exchange. Chest computed tomography (CT) still remains the clinical gold standard for imaging of the lungs, though, in part due to the rapid CT protocols that acquire high-resolution images in seconds and the widespread availability of CT scanners. Quantitative approaches have enabled the extraction of structural lung parenchymal, airway and vascular measurements from chest CT that have been evaluated in many clinical research studies. Together, CT and 129Xe MRI provide complementary information that can be used to evaluate regional lung structure and function, resulting in new insights into lung health and disease. 129Xe MR-CT image registration can be performed to measure regional lung structure-function to better understand lung disease pathophysiology, and to perform image-guided pulmonary interventions. Here, a method for 129Xe MRI-CT registration is outlined to support implementation in research or clinical settings. Registration methods and applications that have been employed to date in the literature are also summarized, and suggestions are provided for future directions that may further overcome technical challenges related to 129Xe MR-CT image registration and facilitate broader implementation of regional lung structure-function evaluation.

Multi-modal Pulmonary Imaging: Using Complementary Information from CT and Hyperpolarized 129Xe MRI to Evaluate Lung Structure-Function

CT and 129Xe MRI provide complementary lung structure-function information that can be exploited for regional analysis using image registration. Here, we provide a protocol that builds from the existing literature for 129Xe MR to CT image registration using open-source platforms.

Hyperpolarized 129Xe gas MRI is an emerging technique to evaluate and measure regional lung function including pulmonary gas distribution and gas ...

In vivo Evaluation of Mucociliary Clearance in Mice

Respiratory motile cilia, specialized organelles of the cell, line the apical surface of epithelial cells lining the respiratory tract. By beating in a metachronal, synchronal fashion, these multiple, motile, actin-based organelles generate a cephalad fluid flow clearing the respiratory tract of inhaled pollutants and pathogens. With increasing environmental pollution, novel viral pathogens and emerging multi-drug resistant bacteria, cilia generated mucociliary clearance (MCC) is essential for maintaining lung health. MCC is also depressed in multiple congenital disorders like primary ciliary dyskinesia, cystic fibrosis as well as acquired disorders like chronic obstructive pulmonary disease. All these disorders have established, in some case multiple, mouse models. In this publication, we detail a method using a small amount of radioactivity and dual-modality SPECT/CT imaging to accurately and reproducibly measure MCC in mice in vivo. The method allows for recovery of mice after imaging, making serial measurements possible, and testing potential therapeutics longitudinally over time. The data in wild-type mice demonstrates the reproducibility of the MCC measurement as long as adequate attention to detail is paid, and the protocol strictly adhered to.

In this publication, we describe protocols for assessing airway mucociliary clearance (MCC) in mice in vivo utilizing dual-modality radionuclide imaging. This protocol is designed for a single photon emission computed tomography (SPECT) and computed tomography (CT) acquisition protocol using mouse whole body (MWB) collimators in a dual SPECT/CT system.

Respiratory motile cilia, specialized organelles of the cell, line the apical surface of epithelial cells lining the respiratory tract. By beating in a ...

Biology

Dynamic Lung Ventilation Assessment with 3D Phase Resolved Functional Lung MRI

Three-Dimensional Phase Resolved Functional Lung Magnetic Resonance Imaging

Pulmonary magnetic resonance imaging (MRI) offers a variety of radiation-free techniques tailored to assess regional lung ventilation or its surrogates. These techniques encompass direct measurements, exemplified by hyperpolarized gas MRI and fluorinated gas MRI, as well as indirect measurements facilitated by oxygen-enhanced MRI and proton-based Fourier decomposition (FD) MRI. In recent times, there has been substantial progress in the field of FD MRI, which involved improving spatial/temporal resolution, refining sequence design and postprocessing, and developing a comprehensive whole-lung approach.
The two-dimensional (2D) phase-resolved functional lung (PREFUL) MRI stands out as an FD-based approach developed for the comprehensive assessment of regional ventilation and perfusion dynamics, all within a single MR acquisition. Recently, a new advancement has been made with the development of 3D PREFUL to assess dynamic ventilation of the entire lung using 8 min exam with a self-gated sequence.
The 3D PREFUL acquisition involves employing a stack-of-stars spoiled-gradient-echo sequence with a golden angle increment. Following the compressed sensing image reconstruction of approximately 40 breathing phases, all the reconstructed respiratory-resolved images undergo registration onto a fixed breathing phase. Subsequently, the ventilation parameters are extracted from the registered images.
In a study cohort comprising healthy volunteers and patients with chronic obstructive pulmonary disease, the 3D PREFUL ventilation parameters demonstrated strong correlations with measurements obtained from pulmonary function tests. Additionally, the interscan repeatability of the 3D PREFUL technique was deemed to be acceptable, indicating its reliability for repeated assessments of the same individuals.
In summary, 3D PREFUL ventilation MRI provides a whole lung coverage and captures ventilation dynamics with enhanced spatial resolution compared to 2D PREFUL. 3D PREFUL technique offers a cost-effective alternative to hyperpolarized 129Xe MRI, making it an attractive option for patient-friendly evaluation of pulmonary ventilation.

Three-dimensional (3D) phase-resolved functional lung (PREFUL) is a functional magnetic resonance imaging (MRI) technique that allows for quantification of regional ventilation of the whole human lung volume, using tidal breathing and contrast-agent free acquisition for 8 min. Here, we present an MR protocol to collect and analyze 3D PREFUL imaging data.

Pulmonary magnetic resonance imaging (MRI) offers a variety of radiation-free techniques tailored to assess regional lung ventilation or its surrogates. ...

Advanced Lung Imaging for Disease Detection and Monitoring

Phase-Resolved Functional Lung MRI for Pulmonary Ventilation and Perfusion (V/Q) Assessment

Fourier decomposition is a contrast agent-free 1H MRI method for lung perfusion (Q) and ventilation (V) assessment. After image registration, the time series of each voxel is analyzed with regard to the cardiac and breathing frequency components.
Using a standard 2D spoiled gradient-echo sequence with a temporal resolution of ~300 ms, an image-sorting algorithm was developed to produce phase-resolved functional lung imaging (PREFUL) with an increased temporal resolution. Thus, it is feasible to evaluate regional flow volume loops (FVL) during tidal volume breathing and depict the propagation of the pulse wave during the cardiac cycle. This method can be applied at 1.5T or 3T with standard MR hardware without the necessity for sequence programming, as the described protocol can be implemented with the default SPGRE sequence on most systems.
PREFUL ventilation MRI has been validated using 129Xe and 19F gas imaging with good regional agreement. Perfusion-weighted PREFUL MRI has been validated using SPECT as well as dynamic contrast enhanced (DCE) MRI. PREFUL has been tested in a dual center dual vendor setting and is currently applied in several ongoing multicenter trials. Furthermore, it is feasible across a range of field strengths (0.55T-3T) and different age groups, including newborns.
Quantitative V/Q PREFUL MRI has been used in patients with cystic fibrosis, chronic obstructive pulmonary disease, chronic thromboembolic pulmonary hypertension, and corona virus disease-2019 to quantify disease and monitor treatment change after therapy. Furthermore, PREFUL V/Q imaging has been shown to predict transplant loss due to chronic lung allograft dysfunction in patients after lung transplantation. In summary, PREFUL MRI is a validated technique for quantitative ventilation and pulmonary pulse wave/perfusion imaging for regional pulmonary disease detection, quantification, and treatment monitoring with potential added value to the current clinical routine.

Author Spotlight: Enhancing Diagnostic Strategies and Biomarker Development for Comprehensive Lung Function Analysis

Here, we describe the implementation of phase-resolved functional lung MRI as a contrast-agent-free proton MR technique for the assessment of pulmonary ventilation and perfusion dynamics. Validated and applicable across different field strengths and age groups, it could enhance clinical decision-making in the future by aiding in disease quantification and therapy monitoring.

Fourier decomposition is a contrast agent-free 1H MRI method for lung perfusion (Q) and ventilation (V) assessment. After image registration, the time ...

Lung CT Segmentation to Identify Consolidations and Ground Glass Areas for Quantitative Assesment of SARS-CoV Pneumonia

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