BCData: A Large-Scale Dataset and Benchmark for Cell Detection and Counting

2020 ◽  
pp. 289-298
Author(s):  
Zhongyi Huang ◽  
Yao Ding ◽  
Guoli Song ◽  
Lin Wang ◽  
Ruizhe Geng ◽  
...  
Keyword(s):  
Large Scale ◽  
Cell Detection ◽  
Large Scale Dataset ◽  
Detection And Counting

scholarly journals ACDC: Automated Cell Detection and Counting for Time-Lapse Fluorescence Microscopy

2020 ◽  
Vol 10 (18) ◽  
pp. 6187
Author(s):  
Leonardo Rundo ◽  
Andrea Tangherloni ◽  
Darren R. Tyson ◽  
Riccardo Betta ◽  
Carmelo Militello ◽  
...  
Keyword(s):  
Large Scale ◽  
Time Lapse ◽  
Cell Counting ◽  
Cell Detection ◽  
Cell Nuclei ◽  
Similarity Coefficients ◽  
Laboratory Practice ◽  
Microscopy Imaging ◽  
Time Lapse Microscopy ◽  
Detection And Counting

Advances in microscopy imaging technologies have enabled the visualization of live-cell dynamic processes using time-lapse microscopy imaging. However, modern methods exhibit several limitations related to the training phases and to time constraints, hindering their application in the laboratory practice. In this work, we present a novel method, named Automated Cell Detection and Counting (ACDC), designed for activity detection of fluorescent labeled cell nuclei in time-lapse microscopy. ACDC overcomes the limitations of the literature methods, by first applying bilateral filtering on the original image to smooth the input cell images while preserving edge sharpness, and then by exploiting the watershed transform and morphological filtering. Moreover, ACDC represents a feasible solution for the laboratory practice, as it can leverage multi-core architectures in computer clusters to efficiently handle large-scale imaging datasets. Indeed, our Parent-Workers implementation of ACDC allows to obtain up to a 3.7× speed-up compared to the sequential counterpart. ACDC was tested on two distinct cell imaging datasets to assess its accuracy and effectiveness on images with different characteristics. We achieved an accurate cell-count and nuclei segmentation without relying on large-scale annotated datasets, a result confirmed by the average Dice Similarity Coefficients of 76.84 and 88.64 and the Pearson coefficients of 0.99 and 0.96, calculated against the manual cell counting, on the two tested datasets.

scholarly journals ACDC: Automated Cell Detection and Counting for Time-lapse Fluorescence Microscopy

2020 ◽  
Author(s):  
Leonardo Rundo ◽  
Andrea Tangherloni ◽  
Darren R. Tyson ◽  
Riccardo Betta ◽  
Carmelo Militello ◽  
...  
Keyword(s):  
Large Scale ◽  
Time Lapse ◽  
Cell Counting ◽  
Cell Detection ◽  
Cell Nuclei ◽  
Similarity Coefficients ◽  
Laboratory Practice ◽  
Microscopy Imaging ◽  
Time Lapse Microscopy ◽  
Detection And Counting

AbstractAdvances in microscopy imaging technologies have enabled the visualization of live-cell dynamic processes using time-lapse microscopy imaging. However, modern methods exhibit several limitations related to the training phases and to time constraints, hindering their application in the laboratory practice. In this work, we present a novel method, named Automated Cell Detection and Counting (ACDC), designed for activity detection of fluorescent labeled cell nuclei in time-lapse microscopy. ACDC overcomes the limitations of the literature methods, by first applying bilateral filtering on the original image to smooth the input cell images while preserving edge sharpness, and then by exploiting the watershed transform and morphological filtering. Moreover, ACDC represents a feasible solution for the laboratory practice, as it can leverage multi-core architectures in computer clusters to efficiently handle large-scale imaging datasets. Indeed, our Parent-Workers implementation of ACDC allows to obtain up to a 3.7× speed-up compared to the sequential counterpart. ACDC was tested on two distinct cell imaging datasets to assess its accuracy and effectiveness on images with different characteristics. We achieved an accurate cell-count and nuclei segmentation without relying on large-scale annotated datasets, a result confirmed by the average Dice Similarity Coefficients of 76.84 and 88.64 and the Pearson coefficients of 0.99 and 0.96, calculated against the manual cell counting, on the two tested datasets.

scholarly journals Joint regression and learning from pairwise rankings for personalized image aesthetic assessment

2021 ◽  
Author(s):  
Jin Zhou ◽  
Qing Zhang ◽  
Jian-Hao Fan ◽  
Wei Sun ◽  
Wei-Shi Zheng
Keyword(s):  
Large Scale ◽  
Assessment Model ◽  
Generic Model ◽  
Small Subset ◽  
Deep Convolutional Neural Networks ◽  
Personal Taste ◽  
Hinge Loss ◽  
Novel Approach ◽  
Large Scale Dataset ◽  
Image Pairs

AbstractRecent image aesthetic assessment methods have achieved remarkable progress due to the emergence of deep convolutional neural networks (CNNs). However, these methods focus primarily on predicting generally perceived preference of an image, making them usually have limited practicability, since each user may have completely different preferences for the same image. To address this problem, this paper presents a novel approach for predicting personalized image aesthetics that fit an individual user’s personal taste. We achieve this in a coarse to fine manner, by joint regression and learning from pairwise rankings. Specifically, we first collect a small subset of personal images from a user and invite him/her to rank the preference of some randomly sampled image pairs. We then search for the K-nearest neighbors of the personal images within a large-scale dataset labeled with average human aesthetic scores, and use these images as well as the associated scores to train a generic aesthetic assessment model by CNN-based regression. Next, we fine-tune the generic model to accommodate the personal preference by training over the rankings with a pairwise hinge loss. Experiments demonstrate that our method can effectively learn personalized image aesthetic preferences, clearly outperforming state-of-the-art methods. Moreover, we show that the learned personalized image aesthetic benefits a wide variety of applications.

scholarly journals VIPPrint: Validating Synthetic Image Detection and Source Linking Methods on a Large Scale Dataset of Printed Documents

2021 ◽  
Vol 7 (3) ◽  
pp. 50
Author(s):  
Anselmo Ferreira ◽  
Ehsan Nowroozi ◽  
Mauro Barni
Keyword(s):  
Large Scale ◽  
State Of The Art ◽  
Child Pornography ◽  
Forensic Analysis ◽  
Synthetic Image ◽  
Image Detection ◽  
Face Images ◽  
Large Scale Dataset ◽  
Scanned Images ◽  
Analysis Of The Images

The possibility of carrying out a meaningful forensic analysis on printed and scanned images plays a major role in many applications. First of all, printed documents are often associated with criminal activities, such as terrorist plans, child pornography, and even fake packages. Additionally, printing and scanning can be used to hide the traces of image manipulation or the synthetic nature of images, since the artifacts commonly found in manipulated and synthetic images are gone after the images are printed and scanned. A problem hindering research in this area is the lack of large scale reference datasets to be used for algorithm development and benchmarking. Motivated by this issue, we present a new dataset composed of a large number of synthetic and natural printed face images. To highlight the difficulties associated with the analysis of the images of the dataset, we carried out an extensive set of experiments comparing several printer attribution methods. We also verified that state-of-the-art methods to distinguish natural and synthetic face images fail when applied to print and scanned images. We envision that the availability of the new dataset and the preliminary experiments we carried out will motivate and facilitate further research in this area.

scholarly journals ShadingNet: Image Intrinsics by Fine-Grained Shading Decomposition

2021 ◽  
Author(s):  
Anil S. Baslamisli ◽  
Partha Das ◽  
Hoang-An Le ◽  
Sezer Karaoglu ◽  
Theo Gevers
Keyword(s):  
Neural Network ◽  
Large Scale ◽  
State Of The Art ◽  
Image Decomposition ◽  
Natural Environments ◽  
Decomposition Algorithms ◽  
Ambient Light ◽  
Fine Grained ◽  
Large Scale Dataset ◽  
Direct Illumination

AbstractIn general, intrinsic image decomposition algorithms interpret shading as one unified component including all photometric effects. As shading transitions are generally smoother than reflectance (albedo) changes, these methods may fail in distinguishing strong photometric effects from reflectance variations. Therefore, in this paper, we propose to decompose the shading component into direct (illumination) and indirect shading (ambient light and shadows) subcomponents. The aim is to distinguish strong photometric effects from reflectance variations. An end-to-end deep convolutional neural network (ShadingNet) is proposed that operates in a fine-to-coarse manner with a specialized fusion and refinement unit exploiting the fine-grained shading model. It is designed to learn specific reflectance cues separated from specific photometric effects to analyze the disentanglement capability. A large-scale dataset of scene-level synthetic images of outdoor natural environments is provided with fine-grained intrinsic image ground-truths. Large scale experiments show that our approach using fine-grained shading decompositions outperforms state-of-the-art algorithms utilizing unified shading on NED, MPI Sintel, GTA V, IIW, MIT Intrinsic Images, 3DRMS and SRD datasets.

scholarly journals Building Damage Detection Using U-Net with Attention Mechanism from Pre- and Post-Disaster Remote Sensing Datasets

2021 ◽  
Vol 13 (5) ◽  
pp. 905
Author(s):  
Chuyi Wu ◽  
Feng Zhang ◽  
Junshi Xia ◽  
Yichen Xu ◽  
Guoqing Li ◽  
...  
Keyword(s):  
Damage Assessment ◽  
Large Scale ◽  
Binary Classification ◽  
Open Data ◽  
Building Damage ◽  
Attention Mechanism ◽  
Large Scale Dataset ◽  
Data Program ◽  
The Impact ◽  
Post Disaster

The building damage status is vital to plan rescue and reconstruction after a disaster and is also hard to detect and judge its level. Most existing studies focus on binary classification, and the attention of the model is distracted. In this study, we proposed a Siamese neural network that can localize and classify damaged buildings at one time. The main parts of this network are a variety of attention U-Nets using different backbones. The attention mechanism enables the network to pay more attention to the effective features and channels, so as to reduce the impact of useless features. We train them using the xBD dataset, which is a large-scale dataset for the advancement of building damage assessment, and compare their result balanced F (F1) scores. The score demonstrates that the performance of SEresNeXt with an attention mechanism gives the best performance, with the F1 score reaching 0.787. To improve the accuracy, we fused the results and got the best overall F1 score of 0.792. To verify the transferability and robustness of the model, we selected the dataset on the Maxar Open Data Program of two recent disasters to investigate the performance. By visual comparison, the results show that our model is robust and transferable.

scholarly journals Towards pixel-to-pixel deep nucleus detection in microscopy images

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Fuyong Xing ◽  
Yuanpu Xie ◽  
Xiaoshuang Shi ◽  
Pingjun Chen ◽  
Zizhao Zhang ◽  
...  
Keyword(s):  
Neural Networks ◽  
Large Scale ◽  
Deep Neural Networks ◽  
Image Data ◽  
Fine Tuning ◽  
Cell Detection ◽  
Imaging Protocol ◽  
Microscopy Image ◽  
Microscopy Images ◽  
Target Data

Abstract Background Nucleus or cell detection is a fundamental task in microscopy image analysis and supports many other quantitative studies such as object counting, segmentation, tracking, etc. Deep neural networks are emerging as a powerful tool for biomedical image computing; in particular, convolutional neural networks have been widely applied to nucleus/cell detection in microscopy images. However, almost all models are tailored for specific datasets and their applicability to other microscopy image data remains unknown. Some existing studies casually learn and evaluate deep neural networks on multiple microscopy datasets, but there are still several critical, open questions to be addressed. Results We analyze the applicability of deep models specifically for nucleus detection across a wide variety of microscopy image data. More specifically, we present a fully convolutional network-based regression model and extensively evaluate it on large-scale digital pathology and microscopy image datasets, which consist of 23 organs (or cancer diseases) and come from multiple institutions. We demonstrate that for a specific target dataset, training with images from the same types of organs might be usually necessary for nucleus detection. Although the images can be visually similar due to the same staining technique and imaging protocol, deep models learned with images from different organs might not deliver desirable results and would require model fine-tuning to be on a par with those trained with target data. We also observe that training with a mixture of target and other/non-target data does not always mean a higher accuracy of nucleus detection, and it might require proper data manipulation during model training to achieve good performance. Conclusions We conduct a systematic case study on deep models for nucleus detection in a wide variety of microscopy images, aiming to address several important but previously understudied questions. We present and extensively evaluate an end-to-end, pixel-to-pixel fully convolutional regression network and report a few significant findings, some of which might have not been reported in previous studies. The model performance analysis and observations would be helpful to nucleus detection in microscopy images.

Large-scale dataset from China gives new insights into leaf margin–temperature relationships

2014 ◽  
Vol 402 ◽  
pp. 73-80 ◽  
Author(s):  
Wen-Yun Chen ◽  
Tao Su ◽  
Jonathan M. Adams ◽  
Frédéric M.B. Jacques ◽  
David K. Ferguson ◽  
...  
Keyword(s):  
Large Scale ◽  
Leaf Margin ◽  
Large Scale Dataset
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