LIVECell—A large-scale dataset for label-free live cell segmentation

AbstractLight microscopy combined with well-established protocols of two-dimensional cell culture facilitates high-throughput quantitative imaging to study biological phenomena. Accurate segmentation of individual cells in images enables exploration of complex biological questions, but can require sophisticated imaging processing pipelines in cases of low contrast and high object density. Deep learning-based methods are considered state-of-the-art for image segmentation but typically require vast amounts of annotated data, for which there is no suitable resource available in the field of label-free cellular imaging. Here, we present LIVECell, a large, high-quality, manually annotated and expert-validated dataset of phase-contrast images, consisting of over 1.6 million cells from a diverse set of cell morphologies and culture densities. To further demonstrate its use, we train convolutional neural network-based models using LIVECell and evaluate model segmentation accuracy with a proposed a suite of benchmarks.

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Real-Time Three-Dimensional Cell Segmentation in Large-Scale Microscopy Data of Developing Embryos

Developmental Cell ◽

10.1016/j.devcel.2015.12.028 ◽

2016 ◽

Vol 36 (2) ◽

pp. 225-240 ◽

Cited By ~ 96

Author(s):

Johannes Stegmaier ◽

Fernando Amat ◽

William C. Lemon ◽

Katie McDole ◽

Yinan Wan ◽

...

Keyword(s):

Real Time ◽

Large Scale ◽

Three Dimensional ◽

Cell Segmentation ◽

Microscopy Data ◽

Dimensional Cell

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Development and study of a method for cell separation during white blood cell segmentation on images of bone marrow preparations in information and measurement systems for diagnostics of acute leukemia

Izmeritel`naya Tekhnika ◽

10.32446/0368-1025it.2020-7-68-72 ◽

2020 ◽

pp. 68-72

Author(s):

V.G. Nikitaev ◽

A.N. Pronichev ◽

V.V. Dmitrieva ◽

E.V. Polyakov ◽

A.D. Samsonova ◽

...

Keyword(s):

Bone Marrow ◽

Blood Cell ◽

Acute Leukemia ◽

White Blood Cell ◽

Cell Separation ◽

Large Scale ◽

Bone Marrow Cells ◽

Automated Analysis ◽

Cell Segmentation ◽

Measurement Systems

The issues of using of information and measurement systems based on processing of digital images of microscopic preparations for solving large-scale tasks of automating the diagnosis of acute leukemia are considered. The high density of leukocyte cells in the preparation (hypercellularity) is a feature of microscopic images of bone marrow preparations. It causes the proximity of cells to eachother and their contact with the formation of conglomerates. Measuring of the characteristics of bone marrow cells in such conditions leads to unacceptable errors (more than 50%). The work is devoted to segmentation of contiguous cells in images of bone marrow preparations. A method of cell separation during white blood cell segmentation on images of bone marrow preparations under conditions of hypercellularity of the preparation has been developed. The peculiarity of the proposed method is the use of an approach to segmentation of cell images based on the watershed method with markers. Key stages of the method: the formation of initial markers and builds the lines of watershed, a threshold binarization, shading inside the outline. The parameters of the separation of contiguous cells are determined. The experiment confirmed the effectiveness of the proposed method. The relative segmentation error was 5 %. The use of the proposed method in information and measurement systems of computer microscopy for automated analysis of bone marrow preparations will help to improve the accuracy of diagnosis of acute leukemia.

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Survey of Clustering Methods for Large Scale Dataset

International Journal of Computer Sciences and Engineering ◽

10.26438/ijcse/v7i5.13381344 ◽

2019 ◽

Vol 7 (5) ◽

pp. 1338-1344

Author(s):

Anupama Jawale ◽

Ganesh Magar

Keyword(s):

Large Scale ◽

Clustering Methods ◽

Large Scale Dataset

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

Computational Visual Media ◽

10.1007/s41095-021-0207-y ◽

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.

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

Journal of Imaging ◽

10.3390/jimaging7030050 ◽

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.

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ShadingNet: Image Intrinsics by Fine-Grained Shading Decomposition

International Journal of Computer Vision ◽

10.1007/s11263-021-01477-5 ◽

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.

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

Remote Sensing ◽

10.3390/rs13050905 ◽

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.

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