Dataset Information

Automatic deep learning-driven label-free image-guided patch clamp system.

ABSTRACT: Patch clamp recording of neurons is a labor-intensive and time-consuming procedure. Here, we demonstrate a tool that fully automatically performs electrophysiological recordings in label-free tissue slices. The automation covers the detection of cells in label-free images, calibration of the micropipette movement, approach to the cell with the pipette, formation of the whole-cell configuration, and recording. The cell detection is based on deep learning. The model is trained on a new image database of neurons in unlabeled brain tissue slices. The pipette tip detection and approaching phase use image analysis techniques for precise movements. High-quality measurements are performed on hundreds of human and rodent neurons. We also demonstrate that further molecular and anatomical analysis can be performed on the recorded cells. The software has a diary module that automatically logs patch clamp events. Our tool can multiply the number of daily measurements to help brain research.

SUBMITTER: Koos K

PROVIDER: S-EPMC7875980 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Automatic deep learning-driven label-free image-guided patch clamp system.

Koos Krisztian K Oláh Gáspár G Balassa Tamas T Mihut Norbert N Rózsa Márton M Ozsvár Attila A Tasnadi Ervin E Barzó Pál P Faragó Nóra N Puskás László L Molnár Gábor G Molnár József J Tamás Gábor G Horvath Peter P

Nature communications 20210210 1

Patch clamp recording of neurons is a labor-intensive and time-consuming procedure. Here, we demonstrate a tool that fully automatically performs electrophysiological recordings in label-free tissue slices. The automation covers the detection of cells in label-free images, calibration of the micropipette movement, approach to the cell with the pipette, formation of the whole-cell configuration, and recording. The cell detection is based on deep learning. The model is trained on a new image datab ...[more]

PMID: 33568670

Similar Datasets

Project description:Chromatin-sensitive Partial Wave Spectroscopic (csPWS) microscopy offers a non-invasive glimpse into the mass density distribution of cellular structures at the nanoscale, leveraging the spectroscopic information. Such capability allows us to analyze the chromatin structure and organization and the global transcriptional state of the cell nuclei for the study of its role in carcinogenesis. Accurate segmentation of the nuclei in csPWS microscopy images is an essential step in isolating them for further analysis. However, manual segmentation is error-prone, biased, time-consuming, and laborious, resulting in disrupted nuclear boundaries with partial or over-segmentation. Here, we present an innovative deep-learning-driven approach to automate the accurate nuclei segmentation of label-free live cell csPWS microscopy imaging data. Our approach, csPWS-seg, harnesses the Convolutional Neural Networks-based U-Net model with an attention mechanism to automate the accurate cell nuclei segmentation of csPWS microscopy images. We leveraged the structural, physical, and biological differences between the cytoplasm, nucleus, and nuclear periphery to construct three distinct csPWS feature images for nucleus segmentation. Using these images of HCT116 cells, csPWS-seg achieved superior performance with a median Intersection over Union (IoU) of 0.80 and a Dice Similarity Coefficient (DSC) score of 0.88. The csPWS-seg overcame the segmentation performance over the baseline U-Net model and another attention-based model, SE-U-Net, marking a significant improvement in segmentation accuracy. Further, we analyzed the performance of our proposed model with four loss functions: binary cross-entropy loss, focal loss, dice loss, and Jaccard loss. The csPWS-seg with focal loss provided the best results compared to other loss functions. The automatic and accurate nuclei segmentation offered by the csPWS-seg not only automates, accelerates, and streamlines csPWS data analysis but also enhances the reliability of subsequent chromatin analysis research, paving the way for more accurate diagnostics, treatment, and understanding of cellular mechanisms for carcinogenesis.

Project description:BackgroundA variety of external factors might seriously degrade PET image quality and lead to inconsistent results. The aim of this study is to explore a potential PET image quality assessment (QA) method with deep learning (DL).MethodsA total of 89 PET images were acquired from Peking Union Medical College Hospital (PUMCH) in China in this study. Ground-truth quality for images was assessed by two senior radiologists and classified into five grades (grade 1, grade 2, grade 3, grade 4, and grade 5). Grade 5 is the best image quality. After preprocessing, the Dense Convolutional Network (DenseNet) was trained to automatically recognize optimal- and poor-quality PET images. Accuracy (ACC), sensitivity, specificity, receiver operating characteristic curve (ROC), and area under the ROC Curve (AUC) were used to evaluate the diagnostic properties of all models. All indicators of models were assessed using fivefold cross-validation. An image quality QA tool was developed based on our deep learning model. A PET QA report can be automatically obtained after inputting PET images.ResultsFour tasks were generated. Task2 showed worst performance in AUC,ACC, specificity and sensitivity among 4 tasks, and task1 showed unstable performance between training and testing and task3 showed low specificity in both training and testing. Task 4 showed the best diagnostic properties and discriminative performance between poor image quality (grade 1, grade 2) and good quality (grade 3, grade 4, grade 5) images. The automated quality assessment of task 4 showed ACC = 0.77, specificity = 0.71, and sensitivity = 0.83, in the train set; ACC = 0.85, specificity = 0.79, and sensitivity = 0.91, in the test set, respectively. The ROC measuring performance of task 4 had an AUC of 0.86 in the train set and 0.91 in the test set. The image QA tool could output basic information of images, scan and reconstruction parameters, typical instances of PET images, and deep learning score.ConclusionsThis study highlights the feasibility of the assessment of image quality in PET images using a deep learning model, which may assist with accelerating clinical research by reliably assessing image quality.

Project description:IntroductionThe primary objective of this study was to develop an end-to-end model that can accurately identify corneal endothelial cells and diagnose keratoconus based on corneal endothelial images acquired from a non-contact specular microscope.MethodsThis was a retrospective case-control study performed at the Refractive Surgery Center of West China Hospital. A total of 403 keratoconus eyes (221 patients) and 370 myopic eyes (185 normal controls) were consecutively recruited from January 2021 to September 2022. Specular microscopy was used to image and measure the morphometric parameters of the corneal endothelial cells. A Fully Convolutional Network model with a ResNet50 (FCN_ResNet50) was established to perform the endothelial segmentation. The images were then classified using an ensemble machine learning system consisting of four pre-trained deep learning networks: DenseNet121, ResNet50, Inception_v3, and MobileNet_v2. The performance of the models was evaluated based on different metrics, such as accuracy, intersection over union (IoU), and mean IoU.ResultsWe established a fully end-to-end deep-learning model for the segmentation of endothelial and diagnosis of keratoconus. For endothelial segmentation, the accuracy of the FCN_ResNet50 model achieved near 90% with mean IoU converging to about 80%. The ensemble machine learning system can achieve over 92% accuracy, and > 98% area under curve (AUC) values to diagnose keratoconus with endothelial cell images. In addition, we constructed a diagnostic model based on deep-learning features and developed an associated nomogram which manifested an excellent performance for diagnosis and monitoring the progression of keratoconus.ConclusionsOur research developed an end-to-end model to automatically identify and assess corneal endothelial morphological changes in keratoconus eyes. Moreover, we also constructed a novel nomogram, which can provide valuable information for the diagnosis, monitoring, and management of the disease.

Dataset Information

Automatic deep learning-driven label-free image-guided patch clamp system.

Publications

Automatic deep learning-driven label-free image-guided patch clamp system.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets