cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j00g3jv7
title: CIL: 54107, Homo sapiens, HeLa. In Cell Image Library

description: Visualization methods: confocal microscopy
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: 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.
DOI: 10.6075/j0qc02k6
title: CIL:12866, Rattus rattus, glandular epithelial cell, milk secreting cell, mammary alveolar cell. In Cell Image Library

description: Immunoelectron microscopy of mammary gland tissue from lactating rats with the trans-Golgi network identified by immunogold labeling of TGN38, a transmembrane trans-golgi protein. Note that trans‐Golgi cisternae in lactating mammary cells contain large amounts of casein and other milk proteins and are grossly expanded due to the osmolarity of the secreted fluid.
description: Preparation: cryostat-sectioned tissue; formaldehyde fixed tissue; embedded tissue; methylcellulose embedded
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain; distribution of a specific protein
Visualization methods: gold; uranyl salt; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: Tissue was processed for immunoelectron microscopy using a modified Tokuyasu method. Briefly, minced tissue was fixed in 4% paraformaldehyde containing 5% sucrose and 100 mM HEPES and infiltrated with PBS containing 2.1 M sucrose over 10 h, with repeated solution changes. Fixed tissue was transferred to an aluminum cryosectioning stub (Ted Pella, Inc., Redding, CA) and immediately frozen in liquid nitrogen. Semithin (90 nm) cryosections were cut at -110C with an UltraCut UCT/FCS cryomicrotome (Leica), using a diamond knife (Diatome) and transferred to a Formvar-coated, carbon-coated, glow-discharged 100-mesh copper-rhodium electron microscopy grid. Following blocking of nonspecific antibody binding sites with 10% calf serum in PBS, the sections were labeled by incubation with an antibody to TGN38 (2F7, mouse monoclonal) followed by colloidal gold-conjugated secondary antibody (10 nm anti-mouse; Ted Pella Inc., Redding, CA) and then negatively stained and embedded with 1% uranyl acetate, 1% methylcellulose in distilled water. Samples were viewed in a Philips CM10 electron microscope, and images were collected digitally. Magnification is 21,000 X. See Ladinsky and Howell (2007) for more information on methods used.
DOI: 10.6075/j0c24vr8
title: CIL:39317, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: The P-face of the ciliary membrane at the base of the cilium has 9 triple rows of IMPs in register with the 9 doublets of the internal axoneme. It is thought that these IMPs may be sites of calcium influx into the base of the cilium for regulating ciliary activity. Also, trichocyst docking sites. TEM taken on 1/6/88 by C. Schroeder with Zeiss 10A operating at 80kV. Neg. 19,800X. 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/).
DOI: 10.6075/j0nz86vq
title: CIL:401, Mus musculus, skeletal muscle cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: uranyl salt; lead salt
Visualization methods: detection of electrons
Processing history: unprocessed raw data
description: Thin section electron microscopy of the gastrocnemius (skeletal) muscle from the delta-sarcoglycan mouse. 

Sample was viewed with a Hitachi 7600 electron microscope (accelerating voltage 80 KV) and imaged with an AMT digital camera. 

This image is part of a set of images of the gastrocnemius muscle from the delta-sarcoglycan knockout mouse. A set of images of wild type mouse gastrocnemius from this same study also are included in The CELL: an image library.

Reference: Nat Med. 2008 Apr;14(4):442-7. 
Genetic and pharmacologic inhibition of mitochondrial-dependent necrosis attenuates muscular dystrophy.
Millay DP, Sargent MA, Osinska H, Baines CP, Barton ER, Vuagniaux G, Sweeney HL, Robbins J, Molkentin JD (tissue preparation described in Fewell JG, et al. A treadmill exercise regimen for identifying cardiovascular phenotypes in transgenic mice. Am J Physiol. 1997;273:H1595–H1605)
DOI: 10.6075/j00p0z0x
title: CIL:24969, Drosophila melanogaster, fat body cell. In Cell Image Library

description: HVEM image of thick section of a polytene chromosome from the fat bodyof 3rd instar larvae of Drosophila melanogaster showing the organization into bands and interbands characteristic of polytene chromosomes. 
 This image was taken with a tilt angle of -5 degrees. The accompanying grouped image, taken at +5 degrees forms a stereo pair, providing a 3D view of the chromosome.
description: Preparation: formaldehyde fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; tungsten compound
Processing history: unprocessed raw data
description: Cells were dissected, fixed with formalin, stained with uranyl acetate, embedded in epoxy resin, and 0.5 micrometer sections prepared
(see Ris H, 1981 Stereoscopic Electron Microscopy of Chromosomes, Meth Cell Biol 22:77-96). Grids were observed using the Madison High Voltage Electron Microscope at 1 MeV.
DOI: 10.6075/j0dj5f56
title: CIL: 52495, 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: One z layer of a z-stack at the given tile position
description: Tile x=5, y=2, z=8 from BL32077_Myc_Terc
DOI: 10.6075/j0qz29qh
title: CIL: 54320, Homo sapiens, HeLa. In Cell Image Library

description: Visualization methods: confocal microscopy
description: CAMK 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/j0mp52d1
title: CIL:13119, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: High resolution quick-freeze deep-etch image of a fracture through the radial canal of the contractile vacuole. This technique presents a picture of a confusing array of non-etchable material surrounding a collecting canal. Lumens of smooth spongiome tubules can be observed. One gets the impression that these tubules are not entirely smooth but that they do have subunits of some sort on their cytosolic surfaces. A few segments of decorated tubules with helically wound subunits on their cytosolic surfaces are visible at the periphery of this radial arm. TEM taken on 5/26/92 by R. Allen with Zeiss 10A operating at 80kV. Neg. 19,800X. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0m32vtx
title: CIL:35897, Saccharomyces cerevisiae. In Cell Image Library

description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Lte1. 
 
 LTE1 is essential for termination of M phase at low temperatures, along with TEM1, and CDC15, all part of the mitotic exit network which is an elaborate signaling system comprising at least eight essential genes: CDC5, CDC14, CDC15, DBF2, DBF20, LTE1, MOB1, and TEM1. LTE1 was originally discovered as a locus essential for growth at 8 C, and was named for this trait as Low Temperature Essential 1. It was later inferred from sequence similarities that LTE1 must code for a guanine nucleotide exchange factor. Genetic evidence suggests that Lte1p activates the GTPase Tem1p which activates the protein kinase Cdc15p. Cdc15p then relieves the inhibition of the protein phosphatase Cdc14p by Net1p, thereby allowing exit from mitosis. In a normal cell cycle, Bub2p bound to Tem1p restrains mitotic exit until the daughter-bound centrosome (with which both Bub2p and Tem1p preferentially associate) comes into contact with Lte1p in the bud, effectively coupling mitotic exit with nuclear segregation. Some evidence suggests that the spatial separation of Tem1p and Lte1p is a key mechanism for controlling the timing of mitotic exit.
 
 These phase,gfp images are part of an image group that ranges from CIL:35880-35899. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the Library.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission; elastic scattering of photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
description: Time-lapse images were collected on a DeltaVision system (Olympus IX71) with 60x/1.42 NA objective at 5 minute intervals. Please see the microscopy section in the referenced manuscript for details for image analysis.
DOI: 10.6075/j0rv0msn
title: CIL:10558, Toxoplasma gondii RH. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image; charge coupled device (CCD)
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: Yellow fluorescent proteins from Aequorea; mRFP1
Processing history: 3D-deconvolution
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
description: A monolayer of human foreskin fibroblast cells was infected with Toxoplasma gondii expressing YFP-tagged Tgalpha1tubulin and mRFP-tagged TgDLC (dynein light chain). Images acquired using API DeltaVision on a Olympus IX70 inverted microscope. Objective: Olympus 60X, 1.4 NA. Filters: EGFP, ex 450-490 em 500-540, mRFP, ex 555-592 em 600-665. Dichromatic mirror: Chroma 89021. Captured with CoolSnapHQ/ICX285. Deconvolved data stack corresponds to raw data stack: CIL# 10557 and DIC image: CIL# 10569.
Unpublished image that is similar to images published in PMID: 16518471. See publication for other experimental details.
DOI: 10.6075/j03b5zkx
title: CIL: 51300, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: A novel cell population analysis to quantify both initial and long-term drug effects, namely pseudopod adaptation and recovery following an initial drug-induced perturbation, adding drug slowly in 1/4 increments over 90 minutes.
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
description: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
DOI: 10.6075/j0b857bk
title: CIL:563, Notophthalmus viridescens, oocyte. In Cell Image Library

description: Amphibian oocytes have many copies of rRNA genes that are actively transcribed. Newt ocyte nuclei were dissected, allowed to swell in a low ionic strength high pH buffer, centrifuged through a sucrose-formaldehyde cushion onto EM grids coated with carbon films, and stained with ethanolic phosphotungstic acid producing a positive stain. In this survey image, the transcribed genes appear tree-like as the closely packed polymerases traverse the gene, and the nascent rRNA transcripts elongate until detached at the termination point.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: microscopy
Imaging mode: transmission electron microscopy (TEM); detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: electron-dense stain; visualization of contiguous regions; tungsten compound
Processing history: unprocessed raw data
DOI: 10.6075/j04x57d5
title: CIL: 53090, 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 1, z=15 from SC_030
DOI: 10.6075/j04x57b8
title: CIL: 52704, 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=7 from PS11_10021_2B_Myc_Terc
description: One z layer of a z-stack at the given tile position
DOI: 10.6075/j0d50m8x
title: CIL:39747, Drosophila melanogaster, early embryonic cell. In Cell Image Library

description: PALM was achieved using a custom wide-field microscope platform with 100x NA 1.4 objective lens or 150X TIRF NA 1.45 lens, yielding a pixel size at the CCD camera of 0.0792 or 0.0528 micrometers respectively.
See also: A Matsuda et al. (2010) Condensed mitotic chromosme structure at nanometer resolution using PALM and EGFP-histones. PLOSone 5:e12768.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: portrayed image
Imaging mode: PALM (photoactivation localization microscopy)
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: PALM reconstruction
Data qualification: Processed
description: (C) Overview of cluster of metaphase chromosomes from a Drosophila embryo visualized using fluorescence microscopy showing the DAPI (blue) and histone (green) fluorescence. (A) PALM image of region in lower box in (A). Red arrowheads point to filamentous structures. 
 See Fig 3 in: A Matsuda et al. (2010) Condensed mitotic chromosme structure at nanometer resolution using PALM and EGFP-histones. PLOSone 5:e12768.
DOI: 10.5281/zenodo.17435458
title: BETA-FOR_SP5_Decomposition_RatCarcass_rapid_assessment_2024-2025

description: This data set contains decomposition rates of rat carcasses on the BETA-FOR rapid assessment patches measured in late summer 2024 and 2025. Rat carcasses were accessible to all invertebrate detritivores (insect_exclusion = False).
description: Variables Description################

*patchLabel_BETAFOR: unique BETA-FOR patch label

*patch: patch number

*subpatch: ID of subpatch located on the patch

*substrate_type: type of sample used, rat = rat carcass

*insect_exclusion: True = sample was covered by an insect net, False = sample was accessible for insects

*start_date: start date of exposure of the sample to patch conditions

*weight_start_wet: wet weight of sample at the start of the exposure 

*end_date: end date of exposure of the sample to patch conditions

*weight_end_wet: wet weight of sample at the end of the exposure

*rat_position: position of rat at the end of the exposure. On_top: rat was found on top of the forest floor, half_soil: rat was dragged half into the soil by decomposers, in_soil: rat was buried completely in the soil, stolen: rat was taken away by vertebrate scavengers

*exposure_time: number of days the samples were exposed to patch conditions

*decomposition_rate: (weight_start_dry - weight_end_dry )/ weight_start_dry

*year: year in which the experiment took place

*insect_exclusion_fail: TRUE: insect net was breached by decomposers, FALSE: insect net was intact, or sample was not covert by insect net

*season: season in which the experiment took place. Removal rates were measured twice, once in spring and once in late summer. 

*data_collector: person collecting the data and supervising field work teams
DOI: 10.5281/zenodo.17435459
title: BETA-FOR_SP5_Decomposition_RatCarcass_rapid_assessment_2024-2025

description: This data set contains decomposition rates of rat carcasses on the BETA-FOR rapid assessment patches measured in late summer 2024 and 2025. Rat carcasses were accessible to all invertebrate detritivores (insect_exclusion = False).
description: Variables Description################

*patchLabel_BETAFOR: unique BETA-FOR patch label

*patch: patch number

*subpatch: ID of subpatch located on the patch

*substrate_type: type of sample used, rat = rat carcass

*insect_exclusion: True = sample was covered by an insect net, False = sample was accessible for insects

*start_date: start date of exposure of the sample to patch conditions

*weight_start_wet: wet weight of sample at the start of the exposure 

*end_date: end date of exposure of the sample to patch conditions

*weight_end_wet: wet weight of sample at the end of the exposure

*rat_position: position of rat at the end of the exposure. On_top: rat was found on top of the forest floor, half_soil: rat was dragged half into the soil by decomposers, in_soil: rat was buried completely in the soil, stolen: rat was taken away by vertebrate scavengers

*exposure_time: number of days the samples were exposed to patch conditions

*decomposition_rate: (weight_start_dry - weight_end_dry )/ weight_start_dry

*year: year in which the experiment took place

*insect_exclusion_fail: TRUE: insect net was breached by decomposers, FALSE: insect net was intact, or sample was not covert by insect net

*season: season in which the experiment took place. Removal rates were measured twice, once in spring and once in late summer. 

*data_collector: person collecting the data and supervising field work teams