Deep Learning-based Segmentation Research Articles

Improving lung nodule segmentation in thoracic CT scans through the ensemble of 3D U-Net models.

The current study explores the application of 3D U-Net architectures combined with Inception and ResNet modules for precise lung nodule detection through deep learning-based segmentation technique. This investigation is motivated by the objective of developing a Computer-Aided Diagnosis (CAD) system for effective diagnosis and prognostication of lung nodules in clinical settings. The proposed method trained four different 3D U-Net models on the retrospective dataset obtained from AIIMS Delhi. To augment the training dataset, affine transformations and intensity transforms were utilized. Preprocessing steps included CT scan voxel resampling, intensity normalization, and lung parenchyma segmentation. Model optimization utilized a hybrid loss function that combined Dice Loss and Focal Loss. The model performance of all four 3D U-Nets was evaluated patient-wise using dice coefficient and Jaccard coefficient, then averaged to obtain the average volumetric dice coefficient (DSCavg) and average Jaccard coefficient (IoUavg) on a test dataset comprising 53 CT scans. Additionally, an ensemble approach (Model-V) was utilized featuring 3D U-Net (Model-I), ResNet (Model-II), and Inception (Model-III) 3D U-Net architectures, combined with two distinct patch sizes for further investigation. The ensemble of models obtained the highest DSCavg of 0.84 ± 0.05 and IoUavg of 0.74 ± 0.06 on the test dataset, compared against individual models. It mitigated false positives, overestimations, and underestimations observed in individual U-Net models. Moreover, the ensemble of models reduced average false positives per scan in the test dataset (1.57 nodules/scan) compared to individual models (2.69-3.39 nodules/scan). The suggested ensemble approach presents a strong and effective strategy for automatically detecting and delineating lung nodules, potentially aiding CAD systems in clinical settings. This approach could assist radiologists in laborious and meticulous lung nodule detection tasks in CT scans, improving lung cancer diagnosis and treatment planning.

Deep Learning-Based Segmentation of Lesions from Wide-Field Vitiligo Images

Evaluation of vitiligo relies on accurate segmentation of lesions, and traditional segmentation methods mainly focus on near-field images. This study proposes a deep learning-based model for accurately segmenting lesions in wide-field vitiligo images. In this study, a dataset of 1267 wide-field vitiligo images was established to train and evaluate segmentation models. A Swin R-CNN model, which combined a Swin Transformer tiny network with a watershed algorithm, was proposed for segmenting lesions. The performances of the Swin R-CNN model and five other models were evaluated and compared through visual and quantitative perspectives. Additionally, the Spearman rank correlation test was performed to analyze result consistency between the Swin R-CNN model and dermatologists in measuring lesion area. The Swin R-CNN model accurately segmented lesions in the wide-field vitiligo images, surpassing other models in both visual and quantitative performance, with an average precision of 84.72% and an average recall of 77.81%. The correlation coefficients between the evaluation results of the Swin R-CNN model and three dermatologists were 0.88, 0.94, and 0.91, respectively. The Swin R-CNN model accurately segments lesions in the wide-field vitiligo images and quantifies lesion area at the dermatologist level. The Swin R-CNN model can provide reliable analytical results for the vitiligo evaluation.

Efficient musculoskeletal annotation using free-form deformation

Traditionally, constructing training datasets for automatic muscle segmentation from medical images involved skilled operators, leading to high labor costs and limited scalability. To address this issue, we developed a tool that enables efficient annotation by non-experts and assessed its effectiveness for training an automatic segmentation network. Our system allows users to deform a template three-dimensional (3D) anatomical model to fit a target magnetic-resonance image using free-form deformation with independent control points for axial, sagittal, and coronal directions. This method simplifies the annotation process by allowing non-experts to intuitively adjust the model, enabling simultaneous annotation of all muscles in the template. We evaluated the quality of the tool-assisted segmentation performed by non-experts, which achieved a Dice coefficient greater than 0.75 compared to expert segmentation, without significant errors such as mislabeling adjacent muscles or omitting musculature. An automatic segmentation network trained with datasets created using this tool demonstrated performance comparable to or superior to that of networks trained with expert-generated datasets. This innovative tool significantly reduces the time and labor costs associated with dataset creation for automatic muscle segmentation, potentially revolutionizing medical image annotation and accelerating the development of deep learning-based segmentation networks in various clinical applications.

Deep learning-based segmentation of left ventricular myocardium on dynamic contrast-enhanced MRI: a comprehensive evaluation across temporal frames.

Cardiac perfusion MRI is vital for disease diagnosis, treatment planning, and risk stratification, with anomalies serving as markers of underlying ischemic pathologies. AI-assisted methods and tools enable accurate and efficient left ventricular (LV) myocardium segmentation on all DCE-MRI timeframes, offering a solution to the challenges posed by the multidimensional nature of the data. This study aims to develop and assess an automated method for LV myocardial segmentation on DCE-MRI data of a local hospital. The study consists of retrospective DCE-MRI data from 55 subjects acquired at the local hospital using a 1.5T MRI scanner. The dataset included subjects with and without cardiac abnormalities. The timepoint for the reference frame (post-contrast LV myocardium) was identified using standard deviation across the temporal sequences. Iterative image registration of other temporal images with respect to this reference image was performed using Maxwell's demons algorithm. The registered stack was fed to the model built using the U-Net framework for predicting the LV myocardium at all timeframes of DCE-MRI. The mean and standard deviation of the dice similarity coefficient (DSC) for myocardial segmentation using pre-trained network Net_cine is 0.78 ± 0.04, and for the fine-tuned network Net_dyn which predicts mask on all timeframes individually, it is 0.78 ± 0.03. The DSC for Net_dyn ranged from 0.71 to 0.93. The average DSC achieved for the reference frame is 0.82 ± 0.06. The study proposed a fast and fully automated AI-assisted method to segment LV myocardium on all timeframes of DCE-MRI data. The method is robust, and its performance is independent of the intra-temporal sequence registration and can easily accommodate timeframes with potential registration errors.

Development and validation of a deep learning-based method for automatic measurement of uterus, fibroid, and ablated volume in MRI after MR-HIFU treatment of uterine fibroids

IntroductionThe non-perfused volume divided by total fibroid load (NPV/TFL) is a predictive outcome parameter for MRI-guided high-intensity focused ultrasound (MR-HIFU) treatments of uterine fibroids, which is related to long-term symptom relief. In current clinical practice, the MR-HIFU outcome parameters are typically determined by visual inspection, so an automated computer-aided method could facilitate objective outcome quantification. The objective of this study was to develop and evaluate a deep learning-based segmentation algorithm for volume measurements of the uterus, uterine fibroids, and NPVs in MRI in order to automatically quantify the NPV/TFL. Materials and MethodsA segmentation pipeline was developed and evaluated using expert manual segmentations of MRI scans of 115 uterine fibroid patients, screened for and/or undergoing MR-HIFU treatment. The pipeline contained three separate neural networks, one per target structure. The first step in the pipeline was uterus segmentation from contrast-enhanced (CE)-T1w scans. This segmentation was subsequently used to remove non-uterus background tissue for NPV and fibroid segmentation. In the following step, NPVs were segmented from uterus-only CE-T1w scans. Finally, fibroids were segmented from uterus-only T2w scans. The segmentations were used to calculate the volume for each structure. Reliability and agreement between manual and automatic segmentations, volumes, and NPV/TFLs were assessed. ResultsFor treatment scans, the Dice similarity coefficients (DSC) between the manually and automatically obtained segmentations were 0.90 (uterus), 0.84 (NPV) and 0.74 (fibroid). Intraclass correlation coefficients (ICC) were 1.00 [0.99, 1.00] (uterus), 0.99 [0.98, 1.00] (NPV) and 0.98 [0.95, 0.99] (fibroid) between manually and automatically derived volumes. For manually and automatically derived NPV/TFLs, the mean difference was 5% [-41%, 51%] (ICC: 0.66 [0.32, 0.85]). ConclusionThe algorithm presented in this study automatically calculates uterus volume, fibroid load, and NPVs, which could lead to more objective outcome quantification after MR-HIFU treatments of uterine fibroids in comparison to visual inspection. When robustness has been ascertained in a future study, this tool may eventually be employed in clinical practice to automatically measure the NPV/TFL after MR-HIFU procedures of uterine fibroids.

Effects of different ground segmentation methods on the accuracy of UAV-based canopy volume measurements.

The nonuniform distribution of fruit tree canopies in space poses a challenge for precision management. In recent years, with the development of Structure from Motion (SFM) technology, unmanned aerial vehicle (UAV) remote sensing has been widely used to measure canopy features in orchards to balance efficiency and accuracy. A pipeline of canopy volume measurement based on UAV remote sensing was developed, in which RGB and digital surface model (DSM) orthophotos were constructed from captured RGB images, and then the canopy was segmented using U-Net, OTSU, and RANSAC methods, and the volume was calculated. The accuracy of the segmentation and the canopy volume measurement were compared. The results show that the U-Net trained with RGB and DSM achieves the best accuracy in the segmentation task, with mean intersection of concatenation (MIoU) of 84.75% and mean pixel accuracy (MPA) of 92.58%. However, in the canopy volume estimation task, the U-Net trained with DSM only achieved the best accuracy with Root mean square error (RMSE) of 0.410 m3, relative root mean square error (rRMSE) of 6.40%, and mean absolute percentage error (MAPE) of 4.74%. The deep learning-based segmentation method achieved higher accuracy in both the segmentation task and the canopy volume measurement task. For canopy volumes up to 7.50 m3, OTSU and RANSAC achieve an RMSE of 0.521 m3 and 0.580 m3, respectively. Therefore, in the case of manually labeled datasets, the use of U-Net to segment the canopy region can achieve higher accuracy of canopy volume measurement. If it is difficult to cover the cost of data labeling, ground segmentation using partitioned OTSU can yield more accurate canopy volumes than RANSAC.

Synthetic Optical Coherence Tomography Angiographs for Detailed Retinal Vessel Segmentation Without Human Annotations.

Optical coherence tomography angiography (OCTA) is a non-invasive imaging modality that can acquire high-resolution volumes of the retinal vasculature and aid the diagnosis of ocular, neurological and cardiac diseases. Segmenting the visible blood vessels is a common first step when extracting quantitative biomarkers from these images. Classical segmentation algorithms based on thresholding are strongly affected by image artifacts and limited signal-to-noise ratio. The use of modern, deep learning-based segmentation methods has been inhibited by a lack of large datasets with detailed annotations of the blood vessels. To address this issue, recent work has employed transfer learning, where a segmentation network is trained on synthetic OCTA images and is then applied to real data. However, the previously proposed simulations fail to faithfully model the retinal vasculature and do not provide effective domain adaptation. Because of this, current methods are unable to fully segment the retinal vasculature, in particular the smallest capillaries. In this work, we present a lightweight simulation of the retinal vascular network based on space colonization for faster and more realistic OCTA synthesis. We then introduce three contrast adaptation pipelines to decrease the domain gap between real and artificial images. We demonstrate the superior segmentation performance of our approach in extensive quantitative and qualitative experiments on three public datasets that compare our method to traditional computer vision algorithms and supervised training using human annotations. Finally, we make our entire pipeline publicly available, including the source code, pretrained models, and a large dataset of synthetic OCTA images.

Deep Learning-Based Segmentation and Risk Stratification for Gastrointestinal Stromal Tumors in Transabdominal Ultrasound Imaging.

To develop a deep neural network system for the automatic segmentation and risk stratification prediction of gastrointestinal stromal tumors (GISTs). A total of 980 ultrasound (US) images from 245 GIST patients were retrospectively collected. These images were randomly divided (6:2:2) into a training set, a validation set, and an internal test set. Additionally, 188 US images from 47 prospective GIST patients were collected to evaluate the segmentation and diagnostic performance of the model. Five deep learning-based segmentation networks, namely, UNet, FCN, DeepLabV3+, Swin Transformer, and SegNeXt, were employed, along with the ResNet 18 classification network, to select the most suitable network combination. The performance of the segmentation models was evaluated using metrics such as the intersection over union (IoU), Dice similarity coefficient (DSC), recall, and precision. The classification performance was assessed based on accuracy and the area under the receiver operating characteristic curve (AUROC). Among the compared models, SegNeXt-ResNet18 exhibited the best segmentation and classification performance. On the internal test set, the proposed model achieved IoU, DSC, precision, and recall values of 82.1, 90.2, 91.7, and 88.8%, respectively. The accuracy and AUC for GIST risk prediction were 87.4 and 92.0%, respectively. On the external test set, the segmentation models exhibited IoU, DSC, precision, and recall values of 81.0, 89.5, 92.8, and 86.4%, respectively. The accuracy and AUC for GIST risk prediction were 86.7 and 92.5%, respectively. This two-stage SegNeXt-ResNet18 model achieves automatic segmentation and risk stratification prediction for GISTs and demonstrates excellent segmentation and classification performance.

Kidney medicine meets computer vision: a bibliometric analysis.

Rapid advances in computer vision (CV) have the potential to facilitate the examination, diagnosis, and treatment of diseases of the kidney. The bibliometric study aims to explore the research landscape and evolving research focus of the application of CV in kidney medicine research. The Web of Science Core Collection was utilized to identify publications related to the research or applications of CV technology in the field of kidney medicine from January 1, 1900, to December 31, 2022. We analyzed emerging research trends, highly influential publications and journals, prolific researchers, countries/regions, research institutions, co-authorship networks, and co-occurrence networks. Bibliographic information was analyzed and visualized using Python, Matplotlib, Seaborn, HistCite, and Vosviewer. There was an increasing trend in the number of publications on CV-based kidney medicine research. These publications mainly focused on medical image processing, surgical procedures, medical image analysis/diagnosis, as well as the application and innovation of CV technology in medical imaging. The United States is currently the leading country in terms of the quantities of published articles and international collaborations, followed by China. Deep learning-based segmentation and machine learning-based texture analysis are the most commonly used techniques in this field. Regarding research hotspot trends, CV algorithms are shifting toward artificial intelligence, and research objects are expanding to encompass a wider range of kidney-related objects, with data dimensions used in research transitioning from 2D to 3D while simultaneously incorporating more diverse data modalities. The present study provides a scientometric overview of the current progress in the research and application of CV technology in kidney medicine research. Through the use of bibliometric analysis and network visualization, we elucidate emerging trends, key sources, leading institutions, and popular topics. Our findings and analysis are expected to provide valuable insights for future research on the use of CV in kidney medicine research.

DSBAV-Net: Depthwise Separable Bottleneck Attention V-Shaped Network with Hybrid Convolution for Left Atrium Segmentation

AbstractAccurate and precise segmentation of the left atrium (LA) is crucial in the early diagnosis and treatment of atrial fibrillation (AF), which is the most common heart rhythm disease in cases. The size of fibrotic tissue in patients with AF is based on manual examination of images obtained from the gadolinium-enhanced cardiac magnetic resonance imaging (MRI) technique. However, manual examination of the acquired images is time-consuming and has many difficulties, such as LA thickness between observers and resolution according to MR devices. To overcome the challenges of manual segmentation of images obtained from MRI devices, end-to-end, fully automated deep learning-based segmentation architectures have become extremely important today. In this study, an encoder–decoder-based V-shaped deep learning architecture is proposed for precise segmentation of LA. In the proposed architecture, standard convolution and depthwise separable convolution are used together. Thus, sparsely connected blocks with fewer parameters and deeply separable convolutions learn the feature representations better, increasing the robustness of the model. In addition, the bottleneck attention module has been added to each encoder layer, allowing the network to learn which features to focus on and which features to suppress in images by attention mapping channel and spatially. The proposed architecture obtained 0.915 dice and 0.844 Jaccard scores in the STACOM 2018 challenge dataset. The obtained results draw attention to the robustness of the model.

Optimizing deep learning-based segmentation of densely packed cells using cell surface markers

BackgroundSpatial molecular profiling depends on accurate cell segmentation. Identification and quantitation of individual cells in dense tissues, e.g. highly inflamed tissue caused by viral infection or immune reaction, remains a challenge.MethodsWe first assess the performance of 18 deep learning-based cell segmentation models, either pre-trained or trained by us using two public image sets, on a set of immunofluorescence images stained with immune cell surface markers in skin tissue obtained during human herpes simplex virus (HSV) infection. We then further train eight of these models using up to 10,000+ training instances from the current image set. Finally, we seek to improve performance by tuning parameters of the most successful method from the previous step.ResultsThe best model before fine-tuning achieves a mean Average Precision (mAP) of 0.516. Prediction performance improves substantially after training. The best model is the cyto model from Cellpose. After training, it achieves an mAP of 0.694; with further parameter tuning, the mAP reaches 0.711.ConclusionSelecting the best model among the existing approaches and further training the model with images of interest produce the most gain in prediction performance. The performance of the resulting model compares favorably to human performance. The imperfection of the final model performance can be attributed to the moderate signal-to-noise ratio in the imageset.

Comparative assessment of established and deep learning-based segmentation methods for hippocampal volume estimation in brain magnetic resonance imaging analysis.

In this study, our objective was to assess the performance of two deep learning-based hippocampal segmentation methods, SynthSeg and TigerBx, which are readily available to the public. We contrasted their performance with that of two established techniques, FreeSurfer-Aseg and FSL-FIRST, using three-dimensional T1-weighted MRI scans (n = 1447) procured from public databases. Our evaluation focused on the accuracy and reproducibility of these tools in estimating hippocampal volume. The findings suggest that both SynthSeg and TigerBx are on a par with Aseg and FIRST in terms of segmentation accuracy and reproducibility, but offer a significant advantage in processing speed, generating results in less than 1 min compared with several minutes to hours for the latter tools. In terms of Alzheimer's disease classification based on the hippocampal atrophy rate, SynthSeg and TigerBx exhibited superior performance. In conclusion, we evaluated the capabilities of two deep learning-based segmentation techniques. The results underscore their potential value in clinical and research environments, particularly when investigating neurological conditions associated with hippocampal structures.

Local and global changes in cell density induce reorganisation of 3D packing in a proliferating epithelium.

Tissue morphogenesis is intimately linked to the changes in shape and organisation of individual cells. In curved epithelia, cells can intercalate along their own apicobasal axes, adopting a shape named 'scutoid' that allows energy minimization in the tissue. Although several geometric and biophysical factors have been associated with this 3D reorganisation, the dynamic changes underlying scutoid formation in 3D epithelial packing remain poorly understood. Here, we use live imaging of the sea star embryo coupled with deep learning-based segmentation to dissect the relative contributions of cell density, tissue compaction and cell proliferation on epithelial architecture. We find that tissue compaction, which naturally occurs in the embryo, is necessary for the appearance of scutoids. Physical compression experiments identify cell density as the factor promoting scutoid formation at a global level. Finally, the comparison of the developing embryo with computational models indicates that the increase in the proportion of scutoids is directly associated with cell divisions. Our results suggest that apico-basal intercalations appearing immediately after mitosis may help accommodate the new cells within the tissue. We propose that proliferation in a compact epithelium induces 3D cell rearrangements during development.

Development and validation of a reliable method for automated measurements of psoas muscle volume in CT scans using deep learning-based segmentation: a cross-sectional study

ObjectivesWe aimed to develop an automated method for measuring the volume of the psoas muscle using CT to aid sarcopenia research efficiently.MethodsWe used a data set comprising the CT scans...

Conquering Class Imbalances in Deep Learning-based Segmentation of Dental Radiographs with Different Loss Functions.

ObjectiveThe imbalanced nature of real-world datasets is an ongoing challenge in the field of machine and deep learning. In medicine and in dentistry, most data samples represent patients not affected by pathologies, and on imagery, pathologic image areas are often smaller than healthy ones. Selecting suitable loss functions during deep learning is essential and may help to overcome the resulting imbalance. We assessed six different loss functions for one exemplary task, tooth structure segmentation on bitewing radiographs, for their performance. MethodsSix different loss functions (Focal Loss, Dice Loss, Tversky Loss and hybrid losses of Cross-Entropy and Dice Loss, Focal and Dice Loss, Focal and Generalized Dice Loss) were compared on a tooth structure segmentation task of 1,625 bitewing radiographs. Training was performed using three different model architectures (U-Net, Linknet, DeepLavbV3+) over a 5-fold cross-validation. Tooth structures consisted of the classes (occurrence in % of samples/captures areas measured on pixel level) enamel (100%/25%), dentin (100%/50%), root canal (100%/10%), filling (81%/8%) and crown (28%/5%). ResultsHybrid loss functions significantly outperformed standalone ones and provided robust results over the different architectures for the classes enamel, dentin, root canal and filling. Specifically, the Dice Focal loss reached high performance to conquer both image level and pixel level class imbalance, respectively. Clinical SignificanceIn dental use cases it is often important to predict minority classes such as pathologies accurately. Using specific loss function may be an effective strategy to overcome data imbalance when training deep learning models.

Feature Sparse Choosing VIT Model for Efficient Concrete Crack Segmentation in Portable Crack Measuring Devices

Concrete crack measurement is important for concrete buildings. Deep learning-based segmentation methods have achieved state-of-art results. However, the model size of these models is extremely large which is impossible to use in portable crack measuring devices. To address this problem, a light-weight concrete crack segmentation model based on the Feature Sparse Choosing VIT (LTNet) is proposed by us. In our proposed model, a Feature Sparse Choosing VIT (FSVIT) is used to reduce computational complexity in VIT as well as reducing the number of channels for crack features. In addition, a Feature Channel Selecting Module (FCSM) is proposed by us to reduce channel features as well as suppressing the influence of interfering features. Finally, Depthwise Separable Convolutions are used to substitute traditional convolutions for further reducing computational complexity. As a result, the model size of our LTNet is extremely small. Experimental results show that our LTNet could achieve an accuracy of 0.887, 0.817 and 0.693, and achieve a recall of 0.882, 0.805 and 0.681 on three datasets, respectively, which is 3–8% higher than current mainstream algorithms. However, the model size of our LTNet is only 2 M.

Distilling Knowledge from a Transformer-Based Crack Segmentation Model to a Light-Weighted Symmetry Model with Mixed Loss Function for Portable Crack Detection Equipment

The detection of cracks is extremely important for maintenance of concrete structures. Deep learning-based segmentation models have achieved high accuracy in crack segmentation. However, mainstream crack segmentation models have very high computational complexity, and therefore cannot be used in portable crack detection equipment. To address this problem, a knowledge distilling structure is designed by us. In this structure, a large teacher model named TBUNet is proposed to transfer crack knowledge to a student model with symmetry structure named ULNet. In the TBUNet, stacked transformer modules are used to capture dependency relationships between different crack positions in feature maps and achieve contextual awareness. In the ULNet, only a tiny U-Net with light-weighted parameters is used to maintain very low computational complexity. In addition, a mixed loss function is designed to ensure detail and global features extracted by the teacher model are consistent with those of the student model. Our designed experiments demonstrate that the ULNet can achieve accuracies of 96.2%, 87.6%, and 75.3%, and recall of 97.1%, 88.5%, and 76.2% on the Cracktree200, CRACK500, and MICrack datasets, respectively, which is 4–6% higher than most crack segmentation models. However, the ULNet only has a model size of 1 M, which is suitable for use in portable crack detection equipment.

Evaluating the relationship between magnetic resonance image quality metrics and deep learning-based segmentation accuracy of brain tumors.

Magnetic resonance imaging (MRI) scans are known to suffer from a variety of acquisition artifacts as well as equipment-based variations that impact image appearance and segmentation performance. It is still unclear whether a direct relationship exists between magnetic resonance (MR) image quality metrics (IQMs) (e.g., signal-to-noise, contrast-to-noise) and segmentation accuracy. Deep learning (DL) approaches have shown significant promise for automated segmentation of brain tumors on MRI but depend on the quality of input training images. We sought to evaluate the relationship between IQMs of input training images and DL-based brain tumor segmentation accuracy toward developing more generalizable models for multi-institutional data. We trained a 3D DenseNet model on the BraTS 2020 cohorts for segmentation of tumor subregions enhancing tumor (ET), peritumoral edematous, and necrotic and non-ET on MRI; with performance quantified via a 5-fold cross-validated Dice coefficient. MRI scans were evaluated through the open-source quality control tool MRQy, to yield 13 IQMs per scan. The Pearson correlation coefficient was computed between whole tumor (WT) dice values and IQM measures in the training cohorts to identify quality measures most correlated with segmentation performance. Each selected IQM was used to group MRI scans as "better" quality (BQ) or "worse" quality (WQ), via relative thresholding. Segmentation performance was re-evaluated for the DenseNet model when (i) training on BQ MRI images with validation on WQ images, as well as (ii) training on WQ images, and validation on BQ images. Trends were further validated on independent test sets derived from the BraTS 2021 training cohorts. For this study, multimodal MRI scans from the BraTS 2020 training cohorts were used to train the segmentation model and validated on independent test sets derived from the BraTS 2021 cohort. Among the selected IQMs, models trained on BQ images based on inhomogeneity measurements (coefficient of variance, coefficient of joint variation, coefficient of variation of the foreground patch) and the models trained on WQ images based on noise measurement peak signal-to-noise ratio (SNR) yielded significantly improved tumor segmentation accuracy compared to their inverse models. Our results suggest that a significant correlation may exist between specific MR IQMs and DenseNet-based brain tumor segmentation performance. The selection of MRI scans for model training based on IQMs may yield more accurate and generalizable models in unseen validation.

Tools and methods for high-throughput single-cell imaging with the mother machine

Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform for single-cell time-lapse imaging is the mother machine, which enables long-term tracking of microbial cells under precisely controlled growth conditions. While several mother machine image analysis pipelines have been developed in the past several years, adoption by a non-expert audience remains a challenge. To fill this gap, we implemented our own software, MM3, as a plugin for the multidimensional image viewer napari. napari-MM3 is a complete and modular image analysis pipeline for mother machine data, which takes advantage of the high-level interactivity of napari. Here, we give an overview of napari-MM3 and test it against several well-designed and widely used image analysis pipelines, including BACMMAN and DeLTA. Researchers often analyze mother machine data with custom scripts using varied image analysis methods, but a quantitative comparison of the output of different pipelines has been lacking. To this end, we show that key single-cell physiological parameter correlations and distributions are robust to the choice of analysis method. However, we also find that small changes in thresholding parameters can systematically alter parameters extracted from single-cell imaging experiments. Moreover, we explicitly show that in deep learning-based segmentation, ‘what you put is what you get’ (WYPIWYG) – that is, pixel-level variation in training data for cell segmentation can propagate to the model output and bias spatial and temporal measurements. Finally, while the primary purpose of this work is to introduce the image analysis software that we have developed over the last decade in our lab, we also provide information for those who want to implement mother machine-based high-throughput imaging and analysis methods in their research.

Tools and methods for high-throughput single-cell imaging with the mother machine.

Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform for single-cell time-lapse imaging is the mother machine, which enables long-term tracking of microbial cells under precisely controlled growth conditions. While several mother machine image analysis pipelines have been developed in the past several years, adoption by a non-expert audience remains a challenge. To fill this gap, we implemented our own software, MM3, as a plugin for the multidimensional image viewer napari. napari-MM3 is a complete and modular image analysis pipeline for mother machine data, which takes advantage of the high-level interactivity of napari. Here, we give an overview of napari-MM3 and test it against several well-designed and widely used image analysis pipelines, including BACMMAN and DeLTA. Researchers often analyze mother machine data with custom scripts using varied image analysis methods, but a quantitative comparison of the output of different pipelines has been lacking. To this end, we show that key single-cell physiological parameter correlations and distributions are robust to the choice of analysis method. However, we also find that small changes in thresholding parameters can systematically alter parameters extracted from single-cell imaging experiments. Moreover, we explicitly show that in deep learning-based segmentation, 'what you put is what you get' (WYPIWYG) - that is, pixel-level variation in training data for cell segmentation can propagate to the model output and bias spatial and temporal measurements. Finally, while the primary purpose of this work is to introduce the image analysis software that we have developed over the last decade in our lab, we also provide information for those who want to implement mother machine-based high-throughput imaging and analysis methods in their research.