Reduced field of view single-shot spiral perfusion imaging

Organoids revealed: morphological analysis of the profound next generation in-vitro model with artificial intelligence

In modern terminology, "organoids" refer to cells that grow in a specific three-dimensional (3D) environment in vitro, sharing similar structures with their source organs or tissues. Observing the morphology or growth characteristics of organoids through a microscope is a commonly used method of organoid analysis. However, it is difficult, time-consuming, and inaccurate to screen and analyze organoids only manually, a problem which cannot be easily solved with traditional technology. Artificial intelligence (AI) technology has proven to be effective in many biological and medical research fields, especially in the analysis of single-cell or hematoxylin/eosin stained tissue slices. When used to analyze organoids, AI should also provide more efficient, quantitative, accurate, and fast solutions. In this review, we will first briefly outline the application areas of organoids and then discuss the shortcomings of traditional organoid measurement and analysis methods. Secondly, we will summarize the development from machine learning to deep learning and the advantages of the latter, and then describe how to utilize a convolutional neural network to solve the challenges in organoid observation and analysis. Finally, we will discuss the limitations of current AI used in organoid research, as well as opportunities and future research directions.

Graphic abstract

Signal intensity informed multi-coil encoding operator for physics-guided deep learning reconstruction of highly accelerated myocardial perfusion CMR

PURPOSE

To develop a physics-guided deep learning (PG-DL) reconstruction strategy based on a signal intensity informed multi-coil (SIIM) encoding operator for highly-accelerated simultaneous multislice (SMS) myocardial perfusion cardiac MRI (CMR).

METHODS

First-pass perfusion CMR acquires highly-accelerated images with dynamically varying signal intensity/SNR following the administration of a gadolinium-based contrast agent. Thus, using PG-DL reconstruction with a conventional multi-coil encoding operator leads to analogous signal intensity variations across different time-frames at the network output, creating difficulties in generalization for varying SNR levels. We propose to use a SIIM encoding operator to capture the signal intensity/SNR variations across time-frames in a reformulated encoding operator. This leads to a more uniform/flat contrast at the output of the PG-DL network, facilitating generalizability across time-frames. PG-DL reconstruction with the proposed SIIM encoding operator is compared to PG-DL with conventional encoding operator, split slice-GRAPPA, locally low-rank (LLR) regularized reconstruction, low-rank plus sparse (L + S) reconstruction, and regularized ROCK-SPIRiT.

RESULTS

Results on highly accelerated free-breathing first pass myocardial perfusion CMR at three-fold SMS and four-fold in-plane acceleration show that the proposed method improves upon the reconstruction methods use for comparison. Substantial noise reduction is achieved compared to split slice-GRAPPA, and aliasing artifacts reduction compared to LLR regularized reconstruction, L + S reconstruction and PG-DL with conventional encoding. Furthermore, a qualitative reader study indicated that proposed method outperformed all methods.

CONCLUSION

PG-DL reconstruction with the proposed SIIM encoding operator improves generalization across different time-frames /SNRs in highly accelerated perfusion CMR.

High spatial resolution spiral first-pass myocardial perfusion imaging with whole-heart coverage at 3 T

PURPOSE

To develop and evaluate a high spatial resolution (1.25 × 1.25 mm² ) spiral first-pass myocardial perfusion imaging technique with whole-heart coverage at 3T, to better assess transmural differences in perfusion between the endocardium and epicardium, to quantify the myocardial ischemic burden, and to improve the detection of obstructive coronary artery disease.

METHODS

Whole-heart high-resolution spiral perfusion pulse sequences and corresponding motion-compensated reconstruction techniques for both interleaved single-slice (SS) and simultaneous multi-slice (SMS) acquisition with or without outer-volume suppression (OVS) were developed. The proposed techniques were evaluated in 34 healthy volunteers and 8 patients (55 data sets). SS and SMS images were reconstructed using motion-compensated L1-SPIRiT and SMS-Slice-L1-SPIRiT, respectively. Images were blindly graded by 2 experienced cardiologists on a 5-point scale (5, excellent; 1, poor).

RESULTS

High-quality perfusion imaging was achieved for both SS and SMS acquisitions with or without OVS. The SS technique without OVS had the highest scores (4.5 [4, 5]), which were greater than scores for SS with OVS (3.5 [3.25, 3.75], P < .05), MB = 2 without OVS (3.75 [3.25, 4], P < .05), and MB = 2 with OVS (3.75 [2.75, 4], P < .05), but significantly higher than those for MB = 3 without OVS (4 [4, 4], P = .95). SMS image quality was improved using SMS-Slice-L1-SPIRiT as compared to SMS-L1-SPIRiT (P < .05 for both reviewers).

CONCLUSION

We demonstrated the successful implementation of whole-heart spiral perfusion imaging with high resolution at 3T. Good image quality was achieved, and the SS without OVS showed the best image quality. Evaluation in patients with expected ischemic heart disease is warranted.

Cardiac real-time MRI using a pre-emphasized spiral acquisition based on the gradient system transfer function

PURPOSE

Segmented Cartesian acquisition in breath hold represents the current gold standard for cardiac functional MRI. However, it is also associated with long imaging times and severe restrictions in arrhythmic or dyspneic patients. Therefore, we introduce a real-time imaging technique based on a spoiled gradient-echo sequence with undersampled spiral k-space trajectories corrected by a gradient pre-emphasis.

METHODS

A fully automatic gradient waveform pre-emphasis based on the gradient system transfer function was implemented to compensate for gradient inaccuracies, to optimize fast double-oblique spiral MRI. The framework was tested in a phantom study and subsequently transferred to compressed sensing-accelerated cardiac functional MRI in real time. Spiral acquisitions during breath hold and free breathing were compared with this reference method for healthy subjects (N = 7) as well as patients (N = 2) diagnosed with heart failure and arrhythmia. Left-ventricular volumes and ejection fractions were determined and analyzed using a Wilcoxon signed-rank test.

RESULTS

The pre-emphasis successfully reduced typical artifacts caused by k-space misregistrations. Dynamic cardiac imaging was possible in real time (temporal resolution < 50 ms) with high spatial resolution (1.34 × 1.34 mm² ), resulting in a total scan time of less than 50 seconds for whole heart coverage. Comparable image quality, as well as similar left-ventricular volumes and ejection fractions, were observed for the accelerated and the reference method.

CONCLUSION

The proposed technique enables high-resolution real-time cardiac MRI with no need for breath holds and electrocardiogram gating, shortening the duration of an entire functional cardiac exam to less than 1 minute.

Whole-heart spiral simultaneous multi-slice first-pass myocardial perfusion imaging

PURPOSE

To develop and evaluate a simultaneous multislice (SMS) spiral perfusion pulse sequence with whole-heart coverage.

METHODS

An orthogonal set of phase cycling angles following a Hadamard pattern was incorporated into a golden-angle (GA) variable density spiral perfusion sequence to perform SMS imaging at different multiband (MB) factors. Images were reconstructed using an SMS extension of L1-SPIRiT that we have termed SMS-L1-SPIRiT. The proposed sequence was evaluated in 40 subjects (10 each for MB factors of 1, 2, 3, and 4). Images were blindly graded by 2 cardiologists on a 5-point scale (5, excellent). To quantitatively evaluate the reconstruction performance against images acquired without SMS, the MB =1 data were used to retrospectively simulate data acquired at MB factors of 2 to 4.

RESULTS

Analysis of the SMS point-spread function for the desired slice showed that the proposed sampling strategy significantly canceled the main-lobe energy of the other slices and has low side-lobe energy resulting in an incoherent temporal aliasing pattern when rotated by the GA. Retrospective experiments demonstrated the SMS-L1-SPIRiT method removed aliasing from the interfering slices and showed excellent agreement with the ground-truth MB =1 images. Clinical evaluation demonstrated high-quality perfusion images with average image-quality scores of 4.3 ± 0.5 (MB =2), 4.2 ± 0.5 (MB =3), and 4.4 ± 0.4 (MB =4) with no significant quality difference in image quality between MB factors (P = 0.38).

CONCLUSION

SMS spiral perfusion at MB factors 2, 3, and 4 produces high-quality perfusion images with whole-heart coverage in a clinical setting with high sampling efficiency.