cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0n8795q
title: CIL:40115, Drosophila melanogaster, embryonic cell. In Cell Image Library

description: Fixation: The media was removed and saved. Then, cell pellets were fixed in 2% glutaraldehyde in 100 mM cacodylate buffer for 30 minutes on ice. The fixed pellet was resuspended in media and centrifuged again. Cells were loaded into the 100 mm well of a type A brass planchette (Ted Pella, Inc. Redding, CA) and fast frozen in the Bal-Tec HPM010 (Bal-Tec, Liechtenstein).

Freeze substitution: After freezing, samples (2) and (3) were placed into a Leica EM AFS Freeze substitution (FS) machine (Leica Microsystems, Bannockburn, IL) and incubated at -90 deg C for 24 hours in 0.1 percent tannic acid in acetone. Samples were washed three times with cold acetone (cooled to -90 degrees C) over 5 minutes, and placed in 1 percent OsO4 and 0.1% UA in cold acetone for 72 hours and held at -90 degrees C. After slowly warming to room temperature at 5 degrees C per hour, the specimens were rinsed in pure acetone three times (10 min. at room temperature). Infiltration and embedding in Durcupan resin was subsequently performed at room temperature.Images were acquired using a JEOL4000EX IVEM, magnification: 30000.0; accelerating voltage: 80.0 keV.
description: Electron micrograph of cultured Drosophila Dl1 cells infected with flock house virus, prepared using chemical fixation and high pressure freezing followed by freeze substitution. This cell was prepared as part of an experiment to investigate different protocols for high pressure freezing. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
description: Preparation: osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Parameter imaged: electron density
Data qualification: Processed
DOI: 10.6075/j09s1r5w
title: CIL:40007, Caulobacter crescentus CB15. In Cell Image Library

description: An image of slice 210 from the reconstructed volume of a tomographic data set from Caulobacter crescentus. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
description: Preparation: osmium tetroxide fixed tissue; cryofixed 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: uranyl salt
Processing history: recorded image
Data qualification: Processed
description: Caulobacter cultures (strain 3724) were cryofixed using a cocktail of 2% Osmium tetroxide, 0.5% uranyl acetate in anhydrous acetone following this time and temperature schedule: -90 Celsius for 72 hours, raised 2 Celsius per hour for 15 hours, held at -60 Celsius for 12 hours, raised 5 Celsius per hour for 12 hours, held at -20 Celsius. Film images were acquired using a JEOL 4000, at a magnification of 30,000X, 400.0 Kv, with the objective aperture set at 2.
DOI: 10.6075/j0x92980
title: CIL:7245, Homo sapiens, epithelial cell. In Cell Image Library

description: HeLa cell in cytokinesis was fixed and stained for microtubules (green), RacGAP1 (red), and DNA (blue). 

Cells were fixed with MeOH on ice for 3 min, and stained with a primary antibody against RacGAP1 (Rac GTPase-activating protein 1), TOPRO3 (Invitrogen) for DNA, and FITC-DM1a antibody against microtubules. Secondary antibody was Alexa 594 for RacGAP1. A single section was collected with a spinning disk microscope on a Nikon TE-2000 with a 1.3 NA 100X objective. Images were collected with an Orca ER CCD camera.
Lasers and filters: Innova 70C Spectrum 3 watt Laser, 488 Laser/ATOF 525/50, 568 Laser/ATOF 605/52, and 647 Laser ATOF 700/75.
description: Preparation: methanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: labeled primary antibody; primary antibody plus labeled secondary antibody; membrane impermeant probe; Fluorescein (FITC); Alexa Fluor 594
Processing history: unprocessed raw data
DOI: 10.6075/j01n7zxn
title: CIL:11489, Rattus, hepatocyte. In Cell Image Library

description: Figures 286 (upper) and 287 (lower) from Chapter 9 (Peroxisomes) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. Peroxidase stained tissue from rat liver showing the normal size and distribution of peroxisomes (upper panel), and an increase in distribution following exposure to [4-chloro-6-(2.3-xylidine) 2-pyrimidinylthio] acetic acid (Wy-14643)(lower panel). Fig. 286 courtesy of Darius Fahimi; Fig. 287, courtesy of Janardan Reddy, from Reddy and Krishnakantha (1975) Science 190:787-9; PMID: 1198095. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
description: Preparation: crosslinking-fixative fixed tissue; embedded 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
Data qualification: Processed
DOI: 10.6075/j0zc82jz
title: CIL: 53755, 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: CMGC 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/j02n51nf
title: CIL:40341, Schlumbergera truncata, pollen. In Cell Image Library

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: 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: Complete specimen preparation protocol available at http://www.dartmouth.edu/~emlab/manuals/sempreps/pollen.html
DOI: 10.6075/j0br8s88
title: CIL:10366, Rattus, multipolar neuron. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; elastic scattering of photons
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
description: Cultured hippocampal neurons after 17 days in vitro, immunostained for MAP2, a microtubule associated protein localized to dendrites (red) but not axons, which are not apparent in the immunofluorescence channel. Both axons, and dendrites, can be seen in the hidden phase micrograph which can be turned on using the edit function in the detailed viewer. Neurons at 10, 14, and 17 days in vitro are represented in this image group. 

Detailed methods: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained for MAP2 (HM2, from Sigma with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 40X lens (HCX PL Fluotar, NA 0.75), Photometrics CoolSnap ES CCD camera and MetaMorph software. A multilayer stack of the fluorescent image of MAP2 staining and the phase image was generated using MetaMorph.
DOI: 10.6075/j01j98wn
title: CIL:10017, Homo sapiens, permanent cell line cell, epithelial cell. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: mRFP1
Processing history: maximum projection
description: Organization of Golgi and endoplasmic reticulum (ER) in a Human HeLa cell expressing Sialyl Transferase-EGFP (green) and Invariant Chain33-mRFP (red). The Sialyl Transferase-EGFP is a Golgi marker and the Invariant Chain33-mRFP is retained in the ER. There are two related files for this specimen: the z series and the maximum projection. This file is the maximum projection.

Zeiss Spinning Disc confocal used with with 220 ms exposure and a 63X oil objective.
DOI: 10.6075/j0j38r4c
title: CIL:47383, Staphylococcus aureus, neutrophil, endothelial cell. In Cell Image Library

description: Visualization of neutrophil recruitment in capillaries proximal to agarose beads. (Figure 5 - Venular data)
description: Mice were anesthetized with ketamine/xylazine, and then subcutaneous tissue on a dorsal flap was exteriorized. GFP staphylococcus aureus beads were inserted. Antibodies were injected into the vasculature to label neutrophils (red) and endothelial cells (blue). Blocking antibodies against the molecule Mac1 were administered after 2 hours of infection.
description: Relation to intact cell: intact cells-in vivo imaging
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Source of contrast: antibody labelling
Processing history: Converted from volocity to .avi
DOI: 10.6075/j0zp45q1
title: CIL: 52837, 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=14 from PS11_167511L_Myc_Terc
description: One z layer of a z-stack at the given tile position
DOI: 10.6075/j0fq9w71
title: CIL: 53018, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Image 2, z=6 from SC_028
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 image
DOI: 10.6075/j0cn73jg
title: CIL: 53529, Homo sapiens, HeLa. In Cell Image Library

description: Visualization methods: confocal microscopy
description: AGC 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.
DOI: 10.6075/j0n0163j
title: CIL: 52709, 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=2, z=12 from PS11_10021_2B_Myc_Terc
description: One z layer of a z-stack at the given tile position
DOI: 10.6075/j0dv1jmv
title: CIL: 54276. In Cell Image Library

description: Visualization methods: confocal microscopy
description: TKL 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.
DOI: 10.25442/hku.30484871
title: Supporting data for manuscript: Wildfire fuel characterization in Hong Kong's subtropical ecosystems

description: My project characterized wildfire fuels in Hong Kong using traditional, field-based, destructive methods. I collected samples from grassland, shrubland, and secondary forest ecosystems in the Kadoorie Farm and Botanic Garden to quantity fuel load, fuel bed depth, bulk density, packing ratio, and moisture content. I collected 9 samples in the grassland and forest plots and 13 samples in the shrubland plot. I uploaded 2 files, one excel sheet with the field measured heights and laboratory measured dry fuel weight. The second excel file contains the calculations of the raw height and weight values to the 5 fuel metrics.
DOI: 10.25442/hku.30484871.v1
title: Supporting data for manuscript: Wildfire fuel characterization in Hong Kong's subtropical ecosystems

description: My project characterized wildfire fuels in Hong Kong using traditional, field-based, destructive methods. I collected samples from grassland, shrubland, and secondary forest ecosystems in the Kadoorie Farm and Botanic Garden to quantity fuel load, fuel bed depth, bulk density, packing ratio, and moisture content. I collected 9 samples in the grassland and forest plots and 13 samples in the shrubland plot. I uploaded 2 files, one excel sheet with the field measured heights and laboratory measured dry fuel weight. The second excel file contains the calculations of the raw height and weight values to the 5 fuel metrics.
DOI: 10.6075/j0s75fwx
title: CIL: 52790, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Tile x=1, y=1, z=9 from PS11_167511L_Myc_Terc
description: One z layer of a z-stack at the given tile position
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
DOI: 10.6075/j04q7tjp
title: CIL: 52557, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Tile x=4, y=4, z=7 from BL32080_Myc_Terc
description: One z layer of a z-stack at the given tile position
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
DOI: 10.6075/j0rn37kg
title: CIL: 54161, Homo sapiens, HeLa. In Cell Image Library

description: Visualization methods: confocal microscopy
description: TK 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.
DOI: 10.6075/j0tq618d
title: CIL: 53937, 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/j0v987qn
title: CIL: 53410, Ceratium sp., Plankton. In Cell Image Library

description: 128x128 segmented image from volumetric hologram
description: Dinoflagellate
description: Imaging mode: Holography
Visualization methods: Amplitude Mode
DOI: 10.6075/j080529p
title: CIL: 53712. In Cell Image Library

description: CMGC 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/j08g8k9v
title: CIL: 52942, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given image
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: Image 2, z=14 from SC_011