Broad Bioimage Benchmark Collection
Names
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Broad Bioimage Benchmark Collection
metasource: Fairsharing.org
version: FAIRsharing.org: BBBC; Broad Bioimage Benchmark Collection; DOI: https://doi.org/10.25504/FAIRsharing.j766zb; Last edited: April 26, 2021, 4:05 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
BBBC
metasource: Fairsharing.org
version: FAIRsharing.org: BBBC; Broad Bioimage Benchmark Collection; DOI: https://doi.org/10.25504/FAIRsharing.j766zb; Last edited: April 26, 2021, 4:05 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Names
More detailed information about this field from each metasource.
Broad Bioimage Benchmark Collection
metasource: Fairsharing.orgversion: FAIRsharing.org: BBBC; Broad Bioimage Benchmark Collection; DOI: https://doi.org/10.25504/FAIRsharing.j766zb; Last edited: April 26, 2021, 4:05 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
BBBC
metasource: Fairsharing.orgversion: FAIRsharing.org: BBBC; Broad Bioimage Benchmark Collection; DOI: https://doi.org/10.25504/FAIRsharing.j766zb; Last edited: April 26, 2021, 4:05 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Names
More detailed information about this field from each metasource.
Broad Bioimage Benchmark Collection
metasource: Fairsharing.orgversion: FAIRsharing.org: BBBC; Broad Bioimage Benchmark Collection; DOI: https://doi.org/10.25504/FAIRsharing.j766zb; Last edited: April 26, 2021, 4:05 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
BBBC
metasource: Fairsharing.orgversion: FAIRsharing.org: BBBC; Broad Bioimage Benchmark Collection; DOI: https://doi.org/10.25504/FAIRsharing.j766zb; Last edited: April 26, 2021, 4:05 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
The Broad Bioimage Benchmark Collection (BBBC) is a collection of freely downloadable microscopy image sets. Researchers are encouraged to use these image sets as reference points when developing, testing, and publishing new image analysis algorithms for the life sciences. In addition to the images themselves, each set includes a description of the biological application and some type of "ground truth" (expected results).
Description
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The Broad Bioimage Benchmark Collection (BBBC) is a collection of freely downloadable microscopy image sets. Researchers are encouraged to use these image sets as reference points when developing, testing, and publishing new image analysis algorithms for the life sciences. In addition to the images themselves, each set includes a description of the biological application and some type of "ground truth" (expected results).
metasource: Fairsharing.orgversion: FAIRsharing.org: BBBC; Broad Bioimage Benchmark Collection; DOI: https://doi.org/10.25504/FAIRsharing.j766zb; Last edited: April 26, 2021, 4:05 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Webpage:
https://data.broadinstitute.org/bbbc/Webpage
More detailed information about this field from each metasource.
https://data.broadinstitute.org/bbbc/
metasource: Fairsharing.orgversion: FAIRsharing.org: BBBC; Broad Bioimage Benchmark Collection; DOI: https://doi.org/10.25504/FAIRsharing.j766zb; Last edited: April 26, 2021, 4:05 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Licence:
Name: BBBC Each image set is assigned its own license, per the image contributorLicence name
More detailed information about this field from each metasource.
BBBC Each image set is assigned its own license, per the image contributor
metasource: Fairsharing.orgversion: FAIRsharing.org: BBBC; Broad Bioimage Benchmark Collection; DOI: https://doi.org/10.25504/FAIRsharing.j766zb; Last edited: April 26, 2021, 4:05 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Licence URL
More detailed information about this field from each metasource.
https://bbbc.broadinstitute.org/
metasource: Fairsharing.orgversion: FAIRsharing.org: BBBC; Broad Bioimage Benchmark Collection; DOI: https://doi.org/10.25504/FAIRsharing.j766zb; Last edited: April 26, 2021, 4:05 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
Annotated high-throughput microscopy image sets for validation
PMID: 22743765
metasource: Fairsharing.org
version: FAIRsharing.org: BBBC; Broad Bioimage Benchmark Collection; DOI: https://doi.org/10.25504/FAIRsharing.j766zb; Last edited: April 26, 2021, 4:05 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Publications
More detailed information about this field from each metasource.
Annotated high-throughput microscopy image sets for validation
PMID: 22743765
metasource: Fairsharing.org
version: FAIRsharing.org: BBBC; Broad Bioimage Benchmark Collection; DOI: https://doi.org/10.25504/FAIRsharing.j766zb; Last edited: April 26, 2021, 4:05 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
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Annotated high-throughput microscopy image sets for validation
PubMed citations: 79.
79 articles citing: Annotated high-throughput microscopy image sets for validation
Capturing Single-Cell Phenotypic Variation via Unsupervised Representation Learning. PMID:35874600
Marker-controlled watershed with deep edge emphasis and optimized H-minima transform for automatic segmentation of densely cultivated 3D cell nuclei. PMID:35864453
Correction of out-of-focus microscopic images by deep learning. PMID:35521557
Deep learning -- promises for 3D nuclear imaging: a guide for biologists. PMID:35420128
Computational analyses of mechanism of action (MoA): data, methods and integration. PMID:35360890
User-Accessible Machine Learning Approaches for Cell Segmentation and Analysis in Tissue. PMID:35360226
An Integrative Segmentation Framework for Cell Nucleus of Fluorescence Microscopy. PMID:35327985
Deep learning for microscopic examination of protozoan parasites. PMID:35284048
A Multiwell-Plate Caenorhabditis elegans Assay for Assessing the Therapeutic Potential of Bacteriophages against Clinical Pathogens. PMID:35171008
Automated detection and staging of malaria parasites from cytological smears using convolutional neural networks. PMID:35036920
Unbox the black-box for the medical explainable AI via multi-modal and multi-centre data fusion: A mini-review, two showcases and beyond. PMID:34980946
TDAExplore: Quantitative analysis of fluorescence microscopy images through topology-based machine learning. PMID:34820649
Development of a chemogenomics library for phenotypic screening. PMID:34819133
Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning. PMID:34795433
CellProfiler 4: improvements in speed, utility and usability. PMID:34507520
DiLFM: an artifact-suppressed and noise-robust light-field microscopy through dictionary learning. PMID:34315860
Multi-stage malaria parasite recognition by deep learning. PMID:34137821
A lossless compression method for multi-component medical images based on big data mining. PMID:34117350
Investigating the Impact of the Bit Depth of Fluorescence-Stained Images on the Performance of Deep Learning-Based Nuclei Instance Segmentation. PMID:34072131
ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis. PMID:34038030
Automated and semi-automated enhancement, segmentation and tracing of cytoskeletal networks in microscopic images: A review. PMID:33995906
A review and comparison of breast tumor cell nuclei segmentation performances using deep convolutional neural networks. PMID:33850222
Deficiency of TMEM53 causes a previously unknown sclerosing bone disorder by dysregulation of BMP-SMAD signaling. PMID:33824347
DeepMIB: User-friendly and open-source software for training of deep learning network for biological image segmentation. PMID:33651804
High Content Analysis Across Signaling Modulation Treatments for Subcellular Target Identification Reveals Heterogeneity in Cellular Response. PMID:33490062
Reproducible image handling and analysis. PMID:33480052
Cell segmentation and tracking using CNN-based distance predictions and a graph-based matching strategy. PMID:33290432
In Situ Classification of Cell Types in Human Kidney Tissue Using 3D Nuclear Staining. PMID:33252180
ALICE: a hybrid AI paradigm with enhanced connectivity and cybersecurity for a serendipitous encounter with circulating hybrid cells. PMID:33042268
TheCellVision.org: A Database for Visualizing and Mining High-Content Cell Imaging Projects. PMID:32934016
Shape-to-graph mapping method for efficient characterization and classification of complex geometries in biological images. PMID:32881897
AnnotatorJ: an ImageJ plugin to ease hand annotation of cellular compartments. PMID:32697683
Keras R-CNN: library for cell detection in biological images using deep neural networks. PMID:32652926
Unprovoked Stabilization and Nuclear Accumulation of the Naked Mole-Rat p53 Protein. PMID:32332849
EVICAN-a balanced dataset for algorithm development in cell and nucleus segmentation. PMID:32239126
A multistep deep learning framework for the automated detection and segmentation of astrocytes in fluorescent images of brain tissue. PMID:32198485
Correcting nuisance variation using Wasserstein distance. PMID:32161688
Quantitative Spatial Analysis of Metabolic Heterogeneity Across in vivo and in vitro Tumor Models. PMID:31737571
Domain-invariant features for mechanism of action prediction in a multi-cell-line drug screen. PMID:31608933
Automated Counting of Cancer Cells by Ensembling Deep Features. PMID:31480740
Applications, promises, and pitfalls of deep learning for fluorescence image reconstruction. PMID:31285623
Deep learning for cellular image analysis. PMID:31133758
CytoPacq: a web-interface for simulating multi-dimensional cell imaging. PMID:31114843
Segmentation of Heavily Clustered Nuclei from Histopathological Images. PMID:30872619
Transfer Learning with Deep Convolutional Neural Networks for Classifying Cellular Morphological Changes. PMID:30641024
Unbiased Phenotype Detection Using Negative Controls. PMID:30616488
Deep Learning in Image Cytometry: A Review. PMID:30565841
EzColocalization: An ImageJ plugin for visualizing and measuring colocalization in cells and organisms. PMID:30361629
Investigating the Relevance of Graph Cut Parameter on Interactive and Automatic Cell Segmentation. PMID:30344617
Environmental properties of cells improve machine learning-based phenotype recognition accuracy. PMID:29973621
CellProfiler 3.0: Next-generation image processing for biology. PMID:29969450
MultiMap: A Tool to Automatically Extract and Analyse Spatial Microscopic Data From Large Stacks of Confocal Microscopy Images. PMID:29875639
Sharing and reusing cell image data. PMID:29851565
Assessing microscope image focus quality with deep learning. PMID:29540156
Morphometrics of complex cell shapes: lobe contribution elliptic Fourier analysis (LOCO-EFA). PMID:29444894
FunImageJ: a Lisp framework for scientific image processing. PMID:29106446
Quality Control for High-Throughput Imaging Experiments Using Machine Learning in Cellprofiler. PMID:29082489
Data-analysis strategies for image-based cell profiling. PMID:28858338
Automated Training of Deep Convolutional Neural Networks for Cell Segmentation. PMID:28798336
Automated analysis of high-content microscopy data with deep learning. PMID:28420678
Systematic and general method for quantifying localization in microscopy images. PMID:27979831
Imagining the future of bioimage analysis. PMID:27926723
Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes. PMID:27560178
'Cytology-on-a-chip' based sensors for monitoring of potentially malignant oral lesions. PMID:27531880
DIC image reconstruction using an energy minimization framework to visualize optical path length distribution. PMID:27453091
SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena. PMID:27412095
Classifying and segmenting microscopy images with deep multiple instance learning. PMID:27307644
CP-CHARM: segmentation-free image classification made accessible. PMID:26817459
Segmentation of Image Data from Complex Organotypic 3D Models of Cancer Tissues with Markov Random Fields. PMID:26630674
Metadata management for high content screening in OMERO. PMID:26476368
Automated Processing of Imaging Data through Multi-tiered Classification of Biological Structures Illustrated Using Caenorhabditis elegans. PMID:25910032
Digital immunohistochemistry wizard: image analysis-assisted stereology tool to produce reference data set for calibration and quality control. PMID:25565221
A comparative study of cell classifiers for image-based high-throughput screening. PMID:25336059
Pipeline for illumination correction of images for high-throughput microscopy. PMID:25228240
Anima: modular workflow system for comprehensive image data analysis. PMID:25126541
Detecting and visualizing cell phenotype differences from microscopy images using transport-based morphometry. PMID:24550445
Benchmark for multi-cellular segmentation of bright field microscopy images. PMID:24195722
Comparison of methods for image-based profiling of cellular morphological responses to small-molecule treatment. PMID:24045582
A call for bioimaging software usability. PMID:22743771
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biological imaging
metasource: Fairsharing.org
version: FAIRsharing.org: BBBC; Broad Bioimage Benchmark Collection; DOI: https://doi.org/10.25504/FAIRsharing.j766zb; Last edited: April 26, 2021, 4:05 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
high-content screen
metasource: Fairsharing.org
version: FAIRsharing.org: BBBC; Broad Bioimage Benchmark Collection; DOI: https://doi.org/10.25504/FAIRsharing.j766zb; Last edited: April 26, 2021, 4:05 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Tags
More detailed information about this field from each metasource.
biological imaging
metasource: Fairsharing.orgversion: FAIRsharing.org: BBBC; Broad Bioimage Benchmark Collection; DOI: https://doi.org/10.25504/FAIRsharing.j766zb; Last edited: April 26, 2021, 4:05 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
high-content screen
metasource: Fairsharing.orgversion: FAIRsharing.org: BBBC; Broad Bioimage Benchmark Collection; DOI: https://doi.org/10.25504/FAIRsharing.j766zb; Last edited: April 26, 2021, 4:05 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
biological imaging high-content screen
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