Evaluation of image quality on low contrast media with deep learning image reconstruction algorithm in prospective ECG-triggering coronary CT angiography.

To assess the impact of low-dose contrast media (CM) injection protocol with deep learning image reconstruction (DLIR) algorithm on image quality in coronary CT angiography (CCTA). In this prospective study, patients underwent CCTA were prospectively and randomly assigned to three groups with different contrast volume protocols (at 320mgI/mL concentration and constant flow rate of 5ml/s). After pairing basic information, 210 patients were enrolled in this study: Group A, 0.7mL/kg (n = 70); Group B, 0.6mL/kg (n = 70); Group C, 0.5mL/kg (n = 70). All patients were examined via a prospective ECG-triggered scan protocol within one heartbeat. A high level DLIR (DLIR-H) algorithm was used for image reconstruction with a thickness and interval of 0.625mm. The CT values of ascending aorta (AA), descending aorta (DA), three main coronary arteries, pulmonary artery (PA), and superior vena cava (SVC) were measured and analyzed for objective assessment. Two radiologists assessed the image quality and diagnostic confidence using a 5-point Likert scale. The CM doses were 46.81 ± 6.41mL, 41.96 ± 7.51mL and 34.65 ± 5.38mL for Group A, B and C, respectively. The objective assessments on AA, DA and the three main coronary arteries and the overall subjective scoring showed no significant difference among the three groups (all p > 0.05). The subjective assessment proved that excellent CCTA images can be obtained from the three different contrast media protocols. There were no significant differences in intracoronary attenuation values between the higher HR subgroup and the lower HR subgroup among three groups. CCTA reconstructed with DLIR could be realized with adequate enhancement in coronary arteries, excellent image quality and diagnostic confidence at low contrast dose of a 0.5mL/kg. The use of lower tube voltages may further reduce the contrast dose requirement.

Deep learning reconstruction CT for liver metastases: low-dose dual-energy vs standard-dose single-energy.

OBJECTIVES: To assess image quality and liver metastasis detection of reduced-dose dual-energy CT (DECT) with deep learning image reconstruction (DLIR) compared to standard-dose single-energy CT (SECT) with DLIR or iterative reconstruction (IR). METHODS: In this prospective study, two groups of 40 participants each underwent abdominal contrast-enhanced scans with full-dose SECT (120-kVp images, DLIR and IR algorithms) or reduced-dose DECT (40- to 60-keV virtual monochromatic images [VMIs], DLIR algorithm), with 122 and 106 metastases, respectively. Groups were matched by age, sex ratio, body mass index, and cross-sectional area. Noise power spectrum of liver images and task-based transfer function of metastases were calculated to assess the noise texture and low-contrast resolution. The image noise, signal-to-noise ratios (SNR) of liver and portal vein, liver-to-lesion contrast-to-noise ratio (LLR), lesion conspicuity, lesion detection rate, and the subjective image quality metrics were compared between groups on 1.25-mm reconstructed images. RESULTS: Compared to 120-kVp images with IR, 40- and 50-keV VMIs with DLIR showed similar noise texture and LLR, similar or higher image noise and low-contrast resolution, improved SNR and lesion conspicuity, and similar or better perceptual image quality. When compared to 120-kVp images with DLIR, 50-keV VMIs with DLIR had similar low-contrast resolution, SNR, LLR, lesion conspicuity, and perceptual image quality but lower frequency noise texture and higher image noise. For the detection of hepatic metastases, reduced-dose DECT by 34% maintained observer lesion detection rates. CONCLUSION: DECT assisted with DLIR enables a 34% dose reduction for detecting hepatic metastases while maintaining comparable perceptual image quality to full-dose SECT. CLINICAL RELEVANCE STATEMENT: Reduced-dose dual-energy CT with deep learning image reconstruction is as accurate as standard-dose single-energy CT for the detection of liver metastases and saves more than 30% of the radiation dose. KEY POINTS: • The 40- and 50-keV virtual monochromatic images (VMIs) with deep learning image reconstruction (DLIR) improved lesion conspicuity compared with 120-kVp images with iterative reconstruction while providing similar or better perceptual image quality. • The 50-keV VMIs with DLIR provided comparable perceptual image quality and lesion conspicuity to 120-kVp images with DLIR. • The reduction of radiation by 34% by DLIR in low-keV VMIs is clinically sufficient for detecting low-contrast hepatic metastases.

Deep learning reconstruction vs standard reconstruction for abdominal CT: the influence of BMI.

OBJECTIVE: This study aimed to evaluate the image quality and lesion conspicuity of the deep learning image reconstruction (DLIR) algorithm compared with standard image reconstruction algorithms on abdominal enhanced computed tomography (CT) scanning with a wide range of body mass indexes (BMIs). METHODS: A total of 112 participants who underwent contrast-enhanced abdominal CT scans were divided into three groups according to BMIs: the 80-kVp group (BMI ≤ 23.9 kg/m2), 100-kVp group (BMI 24-28.9 kg/m2), and 120-kVp group (BMI ≥ 29 kg/m2). All images were reconstructed using filtered back projection (FBP), adaptive statistical iterative reconstruction-V of 50% level (IR), and DLIR at low, medium, and high levels (DL, DM, and DH, respectively). Subjective noise, artifact, overall image quality, and low- and high-contrast hepatic lesion conspicuity were all graded on a 5-point scale. The CT attenuation value (in HU), image noise, and contrast-to-noise ratio (CNR) were quantified and compared. RESULTS: DM and DH improved the qualitative and quantitative parameters compared with FBP and IR for all three BMI groups. DH had the lowest image noise and highest CNR value, while DM had the highest subjective overall image quality and low- and high-contrast lesion conspicuity scores for the three BMI groups. Based on the FBP, the improvement in image quality and lesion conspicuity of DM and DH images was greater in the 80-kVp group than in the 100-kVp and 120-kVp groups. CONCLUSION: For all BMIs, DLIR improves both image quality and hepatic lesion conspicuity, of which DM would be the best choice to balance both. CLINICAL RELEVANCE STATEMENT: The study suggests that utilizing DLIR, particularly at the medium level, can significantly enhance image quality and lesion visibility on abdominal CT scans across a wide range of BMIs. KEY POINTS: • DLIR improved the image quality and lesion conspicuity across a wide range of BMIs. • DLIR at medium level had the highest subjective parameters and lesion conspicuity scores among all reconstruction levels. • On the basis of the FBP, the 80-kVp group had improved image quality and lesion conspicuity more than the 100-kVp and 120-kVp groups.

The value of a deep learning image reconstruction algorithm in whole-brain computed tomography perfusion in patients with acute ischemic stroke.

Background: Computed tomography perfusion (CTP) and computed tomography angiography (CTA) are valuable tools for diagnosing acute ischemic stroke (AIS). It is essential to obtain high-quality CTP and CTA images in short time. This study aimed to evaluate the image quality and diagnostic performance of brain CTP and CTA images generated from CTP reconstructed by a deep learning image reconstruction (DLIR) algorithm on patients with AIS. Methods: The study prospectively enrolled 54 patients with suspected AIS undergoing non-contrast CT and CTP within 24 hours. CTP datasets were reconstructed with three levels of adaptive statistical iterative reconstruction-Veo algorithm [ASIR-V 0% with filtered back projection (FBP), ASIR-V 40%, and ASIR-V 80%] and three levels of DLIR, including low (DLIR-L), medium (DLIR-M), and high (DLIR-H). CTA images were generated using the CTP datasets at the peak arterial phase. Objective parameters including signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), and noise reduction rate. Subjective evaluation was assessed according to Abels scoring system. Perfusion parameters and detection accuracy for infarction core lesions were evaluated. The objective and subjective image quality of CTA images were also evaluated. Results: All reconstructions produced similar CT values (P>0.05). With the increase of ASIR-V and DLIR reconstruction strength, image noise decreased, while SNR and CNR increased for CTP images, especially in white matter. DLIR-H, DLIR-M, and ASIR-V80% yielded higher subjective scores than did ASIR-V40% and FBP. DLIR-H provided the highest noise reduction rate and detection accuracy. No significant difference was found in conventional parameters, the volume of infarct core, or ischemic penumbra among the 6 groups (P>0.05). The objective evaluation of reconstructed CTA images was comparable in DLIR-H, DLIR-M, and ASIR-V80% (P>0.05). The subjective scores of the DLIR-H and DLIR-M images were higher than those of the other groups, especially ASIR-V40% and FBP (P<0.05). Conclusions: Compared with FBP and ASIR-V40%, DLIR-H, DLIR-M, and ASIR-V80% improved the overall image quality of CTP and CTA images to varying degrees. Furthermore, DLIR-H and DLIR-M showed the best performance. DLIR-H is the best choice in diagnosing AIS with improved detection accuracy for cerebral infarction. Reconstructing CTA images using CTP datasets could reduce contrast agent and radiation dose.

Deep learning imaging reconstruction of reduced-dose 40 keV virtual monoenergetic imaging for early detection of colorectal cancer liver metastases.

OBJECTIVE: To explore whether reduced-dose (RD) gemstone spectral imaging (GSI) and deep learning image reconstruction (DLIR) of 40 keV virtual monoenergetic image (VMI) enhanced the early detection and diagnosis of colorectal cancer liver metastases (CRLM). METHODS: Thirty-five participants with pathologically confirmed colorectal cancer were prospectively enrolled from March to August 2022 after routine care abdominal computed tomography (CT). GSI mode was used for contrast-enhanced CT, and two portal venous phase CT images were obtained [standard-dose (SD) CT dose index (CTDIvol) = 15.51 mGy, RD CTDIvol = 7.95 mGy]. The 40 keV-VMI were reconstructed via filtered back projection (FBP) and iterative reconstruction (ASIR-V 60 %, AV60) of both SD and RD images. RD medium-strength deep learning image reconstruction (DLIR-M) and RD high-strength deep learning image reconstruction (DLIR-H) were used to reconstruct the 40 keV-VMI. The contrast-to-noise ratio (CNR) and signal-to-noise ratio (SNR) of the liver and the lesions were objectively evaluated. The overall image quality, lesion conspicuity, and diagnostic confidence were subjectively evaluated, to compare the differences in evaluation results among the different images. RESULTS: All 35 participants (mean age: 59.51 ± 11.01 years; 14 females) underwent SD and RD GSI portal venous-phase CT scans. The dose-length product of the RD GSI scan was reduced by 49-53 % lower than that of the SD GSI scan (420.22 ± 31.95) vs (817.58 ± 60.56). A total of 219 lesions were identified, including 55 benign lesions and 164 metastases, with an average size of 7.37 ± 4.14 mm. SD-FBP detected 207 lesions, SD-AV60 detected 201 lesions, and DLIR-M and DLIR-H detected 199 and 190 lesions, respectively. For lesions ≤ 5 mm, there was no statistical difference between SD-FBP vs DLIR-M (χ2McNemar = 1.00, P = 0.32) and SD-AV60 vs DLIR-M (χ2McNemar = 0.33, P = 0.56) in the detection rate. The CNR, SNR, and noise of DLIR-M and DLIR-H 40 keV-VMI images were better than those of SD-FBP images (P < 0.01) but did not differ significantly from those of SD-AV60 images (P > 0.05). When the lesions ≤ 5 mm, there were statistical differences in the overall diagnostic sensitivity of lesions compared with SD-FBP, SD-AV60, DLIR-M and DLIR-H (P＜0.01). There were no statistical differences in the sensitivity of lesions diagnosis between SD-FBP, SD-AV60 and DLIR-M (both P＞0.05). However, the DLIR-M subjective image quality and lesion diagnostic confidence were higher for SD-FBP (both P < 0.01). CONCLUSION: Reduced dose DLIR-M of 40 keV-VMI can be used for routine follow-up care of colorectal cancer patients, to optimize evaluations and ensure CT image quality. Meanwhile, the detection rate and diagnostic sensitivity and specificity of small lesions, early liver metastases is not obviously reduced.

Is it possible to use low-dose deep learning reconstruction for the detection of liver metastases on CT routinely?

OBJECTIVES: To compare the image quality and hepatic metastasis detection of low-dose deep learning image reconstruction (DLIR) with full-dose filtered back projection (FBP)/iterative reconstruction (IR). METHODS: A contrast-detail phantom consisting of low-contrast objects was scanned at five CT dose index levels (10, 6, 3, 2, and 1 mGy). A total of 154 participants with 305 hepatic lesions who underwent abdominal CT were enrolled in a prospective non-inferiority trial with a three-arm design based on phantom results. Data sets with full dosage (13.6 mGy) and low dosages (9.5, 6.8, or 4.1 mGy) were acquired from two consecutive portal venous acquisitions, respectively. All images were reconstructed with FBP (reference), IR (control), and DLIR (test). Eleven readers evaluated phantom data sets for object detectability using a two-alternative forced-choice approach. Non-inferiority analyses were performed to interpret the differences in image quality and metastasis detection of low-dose DLIR relative to full-dose FBP/IR. RESULTS: The phantom experiment showed the dose reduction potential from DLIR was up to 57% based on the reference FBP dose index. Radiation decreases of 30% and 50% resulted in non-inferior image quality and hepatic metastasis detection with DLIR compared to full-dose FBP/IR. Radiation reduction of 70% by DLIR performed inferiorly in detecting small metastases (< 1 cm) compared to full-dose FBP (difference: -0.112; 95% confidence interval [CI]: -0.178 to 0.047) and full-dose IR (difference: -0.123; 95% CI: -0.182 to 0.053) (p < 0.001). CONCLUSION: DLIR enables a 50% dose reduction for detecting low-contrast hepatic metastases while maintaining comparable image quality to full-dose FBP and IR. KEY POINTS: • Non-inferiority study showed that deep learning image reconstruction (DLIR) can reduce the dose to oncological patients with low-contrast lesions without compromising the diagnostic information. • Radiation dose levels for DLIR can be reduced to 50% of full-dose FBP and IR for detecting low-contrast hepatic metastases, while maintaining comparable image quality. • The reduction of radiation by 70% by DLIR is clinically acceptable but insufficient for detecting small low-contrast hepatic metastases (< 1 cm).

NanoReviser: An Error-Correction Tool for Nanopore Sequencing Based on a Deep Learning Algorithm.

Nanopore sequencing is regarded as one of the most promising third-generation sequencing (TGS) technologies. Since 2014, Oxford Nanopore Technologies (ONT) has developed a series of devices based on nanopore sequencing to produce very long reads, with an expected impact on genomics. However, the nanopore sequencing reads are susceptible to a fairly high error rate owing to the difficulty in identifying the DNA bases from the complex electrical signals. Although several basecalling tools have been developed for nanopore sequencing over the past years, it is still challenging to correct the sequences after applying the basecalling procedure. In this study, we developed an open-source DNA basecalling reviser, NanoReviser, based on a deep learning algorithm to correct the basecalling errors introduced by current basecallers provided by default. In our module, we re-segmented the raw electrical signals based on the basecalled sequences provided by the default basecallers. By employing convolution neural networks (CNNs) and bidirectional long short-term memory (Bi-LSTM) networks, we took advantage of the information from the raw electrical signals and the basecalled sequences from the basecallers. Our results showed NanoReviser, as a post-basecalling reviser, significantly improving the basecalling quality. After being trained on standard ONT sequencing reads from public E. coli and human NA12878 datasets, NanoReviser reduced the sequencing error rate by over 5% for both the E. coli dataset and the human dataset. The performance of NanoReviser was found to be better than those of all current basecalling tools. Furthermore, we analyzed the modified bases of the E. coli dataset and added the methylation information to train our module. With the methylation annotation, NanoReviser reduced the error rate by 7% for the E. coli dataset and specifically reduced the error rate by over 10% for the regions of the sequence rich in methylated bases. To the best of our knowledge, NanoReviser is the first post-processing tool after basecalling to accurately correct the nanopore sequences without the time-consuming procedure of building the consensus sequence. The NanoReviser package is freely available at https://github.com/pkubioinformatics/NanoReviser.

The Landscape of Micro-Inversions Provide Clues for Population Genetic Analysis of Humans.

BACKGROUND: Variations in the human genome have been studied extensively. However, little is known about the role of micro-inversions (MIs), generally defined as small (< 100 bp) inversions, in human evolution, diversity, and health. Depicting the pattern of MIs among diverse populations is critical for interpreting human evolutionary history and obtaining insight into genetic diseases. RESULTS: In this paper, we explored the distribution of MIs in genomes from 26 human populations and 7 nonhuman primate genomes and analyzed the phylogenetic structure of the 26 human populations based on the MIs. We further investigated the functions of the MIs located within genes associated with human health. With hg19 as the reference genome, we detected 6968 MIs among the 1937 human samples and 24,476 MIs among the 7 nonhuman primate genomes. The analyses of MIs in human genomes showed that the MIs were rarely located in exonic regions. Nonhuman primates and human populations shared only 82 inverted alleles, and Africans had the most inverted alleles in common with nonhuman primates, which was consistent with the "Out of Africa" hypothesis. The clustering of MIs among the human populations also coincided with human migration history and ancestral lineages. CONCLUSIONS: We propose that MIs are potential evolutionary markers for investigating population dynamics. Our results revealed the diversity of MIs in human populations and showed that they are essential to construct human population relationships and have a potential effect on human health.