cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j06h4h40
title: CIL: 54029, Homo sapiens, HeLa. In Cell Image Library

description: STE family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
description: Visualization methods: confocal microscopy
DOI: 10.6075/j070809p
title: CIL:40554, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; tissue in vitreous ice embedment; microtome-sectioned tissue; monoclonal antibodies
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density; intrinsic mass distribution
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; uranyl salt; gold
Processing history: recorded image; film
Data qualification: Raw;spatialmeasurements
description: To label membranes inside the cell we used very lightly fixed cells (0.25% glutaraldehyde) that were then rapidly frozen in liquid nitrogen and sectioned later at -100oC. These frozen sections were picked up on drops of methylcellulose and transferred to a Formvar-supported grid. The sections were immunogold labeled (15nm gold) to show the location of the specific antigen inside the cell as well as on the cell surface. Microtome sections prepared at approximately 75nm thickness. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Monoclonal antibody for antigen B2 (called mAb PC-1 in Fok et al., Eur. J. Cell Biol. 40:1-8, 1986) is located on the cytopharynx and along the cytopharyngeal ribbons. It can be seen here on the DV-I membrane that is detached from the cytopharynx. Some acidosomes have already fused with this phagosome. The unfused acidosomes are not labeled with this mAb. TEM taken on 4/3/87 by R. Allen with Zeiss 10A operating at 80kV. Neg. 12,000X. Part published in J. Cell Sci. 108:1263-1274, 1995. Adapted with permission.
DOI: 10.6075/j0d21wpz
title: CIL:2828, Caenorhabditis elegans. In Cell Image Library

description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 8 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
DOI: 10.6075/j0c24vh4
title: CIL:16460, Prochloron. In Cell Image Library

description: Prochloron was collected at Coconut Island, Oahu, Hawaii. Green colonies of didemnid ascidians, Diplosoma virens, were collected from shallow waters. Green spherical cells, identified as Prochloron, were released from the ascidians by gently pressing on the colonies while flushing the surface with sea water. Cells were centrifuged, then rinsed in filtered sea water fixed with glutaraldehyde, infiltrated with glycerol and vitrified. Samples were fractured and replicated using a Balzers BA 360 freeze-etch device and examined and in a JEOL 100C TEM at 50,000X magnification. Images were recorded on film and digitized.
description: Freeze-fracture replica of the unicellular photosynthetic prokaryote Prochloron showing the distribution and size of particles on cleaved thylakoid membranes. 
This image group includes many other freeze-fracture images of Prochloron.

See also: Giddings TH, Withers NW, Staehelin LA.1980 Supramolecular structure of stacked and unstacked regions of the photosynthetic membranes of Prochloron sp., a prokaryote. Proc Natl Acad Sci U S A. 77:352-3566.
description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: whole mounted tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0cv4hbp
title: CIL: 52827, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: Tile x=4, y=1, z=4 from PS11_167511L_Myc_Terc
description: One z layer of a z-stack at the given tile position
DOI: 10.6075/j0xk8f77
title: CIL: 53914, Homo sapiens, HeLa. In Cell Image Library

description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
description: OTHER family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
description: Visualization methods: confocal microscopy
DOI: 10.6075/j0445kv6
title: CIL: 50761, Drosophila melanogaster. In Cell Image Library

description: We show in this study that brain and intestinal stem cells of Drosophila contain a new type of cytoplasmic protrusion which is enriched in mitochondria and that the mitochondria are probably dependent on microtubules for their distribution. The protrusions form mitochondria-enriched cytoplasmic bridges from the stem cells to their niche that we speculate are important in regulating stem cell quiescence and activation.
description: Specimen preparation: Larval brains (LBs) were prepared from starved (amino acid-restricted) first instar (L1) larvae to enrich for quiescent neural stem cells. The LBs were glutaraldehyde-fixed, tannic acid and OsO4-stained, embedded in resin, thin-sectioned (60-70 nm) and stained with uranyl acetate/lead citrate, then observed by TEM.
description: Imaging mode: DICM
Visualization methods: Spinning disc confocal DICM & widefield DICM Using a Nikon TiE microscope equipped with a 40x, 0.95 N.A. objective and a Hamamatsu ORCA-Flash 4.0 V3 Digital CMOS camera, or a Nikon TiE spinning-disc confocal microscope equipped with a Yokogawa CSU-X1 scanning unit, an Andor iXon 888 EMCCD camera, and a 60x, 1.3 N.A. water-immersion objective or a 40x, 0.95 N.A. objective
DOI: 10.6075/j0125rt6
title: CIL:13193, Haemanthus katharinae, endosperm. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: elastic scattering of electrons
Visualization methods: uranyl salt
Processing history: unprocessed raw data
description: Dividing cells from the liquid endosperm of the lily Haemanthus katherinae were fixed with paraformaldehye, embedded in epoxy, and 1.0 micrometer sections prepared. Images were obtained with the Wisconsin high voltage TEM at 1MEV. For this low magnification survey micrograph of chromosomes at anaphase, the grid was tilted to 40 degrees. A similar micrograph tilted to 60 degrees is grouped with this image, making a stereo pair that provides an oblique 3D view.
DOI: 10.6075/j00z72xp
title: CIL: 53399, Plankton. In Cell Image Library

description: 128x128 segmented image from volumetric hologram
description: Choanoflagellate
description: Imaging mode: Holography
Visualization methods: Amplitude Mode
DOI: 10.15468/dl.mxqvku
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Allium fistulosum"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009617-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0b27t0t
title: CIL:16311, Maize mosaic virus, Zea mays, plant cell. In Cell Image Library

description: Preparation: tissue in epoxy resin embedment; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: osmium tetroxide; lead salt; uranyl salt
Data qualification: Processed
description: The images in this group show electron micrographs of epidermal and mesophyll cells in thin sections of maize leaves infected with Maize mosaic virus (MMV, Rhabdoviridae). MMV virions are bullet-shaped or bacilliform, 186-213 nm long and ca. 61 nm in diameter. This jpg image is of a mesophyll leaf cell from a maize plant infected with Maize mosaic virus (MMV), and is identical to the unlabeled tif file CIL:12417. MMV virions (v), budding through the inner nuclear membrane (inm), are accumulating between this membrane and the outer nuclear membrane (onm) as well as in intracytoplasmic vesicles, sometimes forming crystalline arrays. Ch=chloroplast; cw=cell wall; cy=cytoplasm; N=nucleus, va=cell vacuole
Detailed methods: Pieces of leaves were processed for TEM by fixation in glutaraldehyde and osmium tetroxide, embedded in Spurr's medium. Thin sections were stained with uranyl acetate and lead citrate, and examined by a Philips-201 TEM (non-digital camera). Negatives were scanned later to generate these electronic files. See E.-D. Ammar et al. (2005) J. Phytopathology, 153:129-136.
.
DOI: 10.6075/j06m35jw
title: CIL:16312, Maize mosaic virus, Zea mays, plant cell, epidermal cell. In Cell Image Library

description: The images in this group show electron micrographs of epidermal and mesophyll cells in thin sections of maize leaves infected with Maize mosaic virus (MMV, Rhabdoviridae). This jpg image is of an epidermal leaf cell from a maize plant infected with Maize mosaic virus (MMV), and is identical to the unlabeled tif file CIL:12414. MMV virions are bullet-shaped or bacilliform, 186-213 nm long and ca. 61 nm in diameter. In infected cells, MMV virions bud through nuclear membranes and accumulate in perinuclear spaces or in intracytoplasmic vesicles. Massive arrays of MMV virions (v), budding through the nuclear membranes, surround the nucleus (N) and occupy most of the cell cytoplasm. iw=inner cell wall; ow=outer cell wall; m=mitochondrion.
Detailed methods: Pieces of leaves were processed for TEM by fixation in glutaraldehyde and osmium tetroxide, embedded in Spurr's medium. Thin sections were stained with uranyl acetate and lead citrate, and examined by a Philips-201 TEM (non-digital camera). Negatives were scanned later to generate these electronic files. See E.-D. Ammar et al. (2005) J. Phytopathology, 153:129-136.
description: Preparation: tissue in epoxy resin embedment; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: osmium tetroxide; lead salt; uranyl salt
Data qualification: Processed
DOI: 10.6075/j028074h
title: CIL: 52488, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Tile x=5, y=2, z=1 from BL32077_Myc_Terc
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: One z layer of a z-stack at the given tile position
DOI: 10.6075/j0q23zf6
title: CIL:9170, Homo sapiens, permanent cell line cell, epithelial cell. In Cell Image Library

description: Preparation: unfixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: unprocessed raw data
description: Sialyl Transferase-EGFP transfected HeLa cells demonstrating the redistribution of the Golgi Apparatus to the Endoplasmic Reticulum upon treatment with Brefeldin A (BFA). 
Images were collected as a 4D time series (z-stack over time). z-stacks of 48 individual timepoints are included in this collection of files as well as the movie SiEGFP_BFA.avi, which is the maximum projection of the z-stacks at the individual time points.

BFA was added according to the following protocol:
Timepoint1: Before addition of BFA 0seconds (8 Z-slices at 1 um apart)
Timepoint2: After addition of BFA 130seconds (8 Z-slices at 1 um apart) 
Timepoint3: 238 seconds (11 Z-slices at 1 um apart) 
Timepoint3 thru Timepoint48: Images captured every 5 seconds (11 Z-slices at 1 um apart at each time point) 

Images were collected on a Carl Zeiss spinning disk confocal with a 63X 1.4 NA objective with 250 ms exposures at 5 s intervals.
DOI: 10.5281/zenodo.17277465
title: DORIE: Dataset of Road Infrastructure Elements

description: DORIE is a novel, high-resolution object detection dataset specifically curated for real-time patrol vehicle monitoring and automated road infrastructure inspection. This dataset addresses a significant gap in existing driving benchmarks by focusing explicitly on safety-critical static infrastructure elements that are often underrepresented. The dataset is designed to facilitate the training and evaluation of object detection models for classes crucial to road safety and maintenance.

Key Data Characteristics



Total Images: 938 manually annotated images.

Total Object Instances: Over 6,800 object instances.

Annotation Type: Manually annotated with YOLO bounding boxes.

Resolution: High resolution at 5,568 x 4,872.

Collection Site: Collected along the A2 motorway in Spain (from Madrid to the boundary between the provinces of Guadalajara and Soria). The road section is maintained by Acciona Construction S.A.

Collection Setup: Acquired using a GoPro HERO13 Black mounted on the hood of a patrol vehicle, simulating the viewpoint of a typical dash camera.

Inherent Challenges: The dataset includes real-world challenges such as small object size, class imbalance, varying lighting and weather (including high sun glare), and occlusion by other vehicles or environmental elements.


Annotated Classes

DORIE features ten safety-critical categories, including both static infrastructure and dynamic traffic participants:



Bollard: Roadside safety posts or poles. 

Delineator: Reflective roadside markers used to guide traffic.

Prohibitory sign: Standard traffic prohibition signs (circular signs with a white background and red border). 

Danger sign: Warning signs indicating hazards ahead (triangular signs with a white background and red border). 

Mandatory sign: Signs prescribing specific driving actions (circular signs with a blue background). 

Other sign: Additional traffic signs not falling into the previous groups. 

Guardrail: Roadside safety barriers.

Road: The drivable road surface. 

Car: Passenger vehicles visible on the road. 

Truck: Larger vehicles such as lorries and freight trucks.


Dataset Split

The dataset is split into training, validation, and test subsets to facilitate standardized model development and evaluation:



Total Instances: 6,852

Training Set: 4,408 instances

Validation Set: 1,081 instances

Test Set: 1,363 instances


Funding

This work was supported by the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement No 955356 (Improved Robotic Platform to perform Maintenance and Upgrading Roadworks: The HERON Approach)
DOI: 10.5281/zenodo.17277466
title: DORIE: Dataset of Road Infrastructure Elements

description: DORIE is a novel, high-resolution object detection dataset specifically curated for real-time patrol vehicle monitoring and automated road infrastructure inspection. This dataset addresses a significant gap in existing driving benchmarks by focusing explicitly on safety-critical static infrastructure elements that are often underrepresented. The dataset is designed to facilitate the training and evaluation of object detection models for classes crucial to road safety and maintenance.

Key Data Characteristics



Total Images: 938 manually annotated images.

Total Object Instances: Over 6,800 object instances.

Annotation Type: Manually annotated with YOLO bounding boxes.

Resolution: High resolution at 5,568 x 4,872.

Collection Site: Collected along the A2 motorway in Spain (from Madrid to the boundary between the provinces of Guadalajara and Soria). The road section is maintained by Acciona Construction S.A.

Collection Setup: Acquired using a GoPro HERO13 Black mounted on the hood of a patrol vehicle, simulating the viewpoint of a typical dash camera.

Inherent Challenges: The dataset includes real-world challenges such as small object size, class imbalance, varying lighting and weather (including high sun glare), and occlusion by other vehicles or environmental elements.


Annotated Classes

DORIE features ten safety-critical categories, including both static infrastructure and dynamic traffic participants:



Bollard: Roadside safety posts or poles. 

Delineator: Reflective roadside markers used to guide traffic.

Prohibitory sign: Standard traffic prohibition signs (circular signs with a white background and red border). 

Danger sign: Warning signs indicating hazards ahead (triangular signs with a white background and red border). 

Mandatory sign: Signs prescribing specific driving actions (circular signs with a blue background). 

Other sign: Additional traffic signs not falling into the previous groups. 

Guardrail: Roadside safety barriers.

Road: The drivable road surface. 

Car: Passenger vehicles visible on the road. 

Truck: Larger vehicles such as lorries and freight trucks.


Dataset Split

The dataset is split into training, validation, and test subsets to facilitate standardized model development and evaluation:



Total Instances: 6,852

Training Set: 4,408 instances

Validation Set: 1,081 instances

Test Set: 1,363 instances


Funding

This work was supported by the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement No 955356 (Improved Robotic Platform to perform Maintenance and Upgrading Roadworks: The HERON Approach)
DOI: 10.6075/j04b30mb
title: CIL:40331, Schlumbergera truncata, pollen. In Cell Image Library

description: Scanning electron micrograph of Schlumbergera truncata (Christmas cactus) pollen. These specimens have been acetolyzed to remove cytoplasm and pollenkit in order to reveal the intricate wall structure. This is part of a large image collection of scanning electron micrographs of pollen samples. Images of a particular species are grouped together. However, to find images and groups of images from other species, please search for the the name of the contributor, Louisa Howard.
description: Preparation: acetolysis
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in deposition of metal shadow
Visualization methods: gold
Processing history: unprocessed raw data
description: Complete specimen preparation protocol available at http://www.dartmouth.edu/~emlab/manuals/sempreps/pollen.html