cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17467303
title: Dataset for the BIA Ireland study

description: This dataset contains the data produced in the Business Impact Assessment for Obesity and Population Nutrition and the Business Impact Assessment for Sustainability that were conducted in Ireland in 2023-2024, following the protocols established by INFORMAS (INFORMAS | International Network for Food and Obesity/non-communicable Disease Research, Monitoring and Action Support). A total of thirty-five companies were assessed. The dataset includes each company’s score in all BIA domains and indicators, together with screenshots showing the relevant information on company commitments. In some cases, information was found in company publications such as reports or brochures. These publications cannot be posted publicly but can be made available on request. Where applicable, a list of these documents is included.  The full report of the BIAs in Ireland can be found at https://zenodo.org/records/14513316, and the executive summary can be downloaded at https://zenodo.org/records/14513255.
DOI: 10.6075/j0hx1cf5
title: CIL: 54513, 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: Visualization methods: confocal microscopy
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.
DOI: 10.6075/j0mp52z6
title: CIL: 54015, 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: 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: Visualization methods: confocal microscopy
DOI: 10.6075/j0n29w3j
title: CIL:16235, 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: 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
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.
DOI: 10.6075/j0k073b3
title: CIL:16234, 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/j0w95924
title: CIL: 54754, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: DAPI staining
description: Imaging mode: fluorescence microscopy
Visualization methods: epifluorescent imaging
description: Epifluorescent imaging
DOI: 10.6075/j00r9nr5
title: CIL:39534, Saccharomyces cerevisiae. In Cell Image Library

description: The images were acquired using a 60x 1.42 NA objective lens on Delta Vision system equipped with CoolSNAP_HQ2 / HQ2-ICX285. Please see the microscopy section in the referenced manuscript for details for image analysis.
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Cdc6. Cdc 6 is an essential ATP-binding protein required for DNA replication, component of the pre-replicative complex (pre-RC) which requires ORC to associate with chromatin and is in turn required for Mcm2-7p DNA association; homologous to S. pombe Cdc18p.These phase,gfp z-series images are part of an image group that ranges from CIL:39531-39535. 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
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0xs5vj5
title: CIL:48010, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Single computed slice through a tomographic reconstruction of a selectively-stained spiny dendrite. This medium spiny neuron was contained in a thick section from the neostriatum of a dopamine transporter knock out mouse. The reconstructed image has been downsampled from the raw data image, which can be accessed using the link provided to the Cell Centered Database.
description: Micer were C57BL/129SvJ. Individual cells in fixed tissue were injected with Lucifer yellow and stored in 4% paraformaldehyde at 4° C. Fluorescence was photoconverted using DAB and a confocal laser light source. After this process, tissue was washed thoroughly in PBS and processed for EM by osmication, dehydration, and embedding in epoxy resin. For detailed methods, see the protocol provided in the CCDB. The tomogram was generated using an Hitachi 3MeV UHVEM. Single tilt images spanned -70 to 70° in 2° increments.
description: Preparation: formaldehyde fixed tissue; glutaraldehyde fixed tissue; tissue in epoxy resin embedment; osmium tetroxide fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: detection of electrons; illumination by electrons
Parameter imaged: electron density
Visualization methods: intracellular filling
Data qualification: Processed
DOI: 10.6075/j0c828b5
title: CIL:7051, Mus musculus, permanent cell line cell, fibroblast. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: structured illumination microscopy (SIM)
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: EGFP
Processing history: unprocessed raw data
description: NIH 3T3 cell expressing EGFP-Lifeact (a small genetically expressed probe that binds to actin and is derived from the first 17 aa of Abp140) imaged with structured illumination. Structured illumination produces images that have a lateral resolution of approximately 100 nm, or twice the diffraction limited 200 nm resolution of conventional fluorescent microscopy techniques. 

There are three related images in this folder. This file is the raw data. The 5 positions of the illumination grid pattern are visible in the 10 slices of the z-series. The structure of this file is that all 150 images appear as a horizontally incrementing sequence. The second file is a z-series of six of the reconstructed structured illumination images. The third file contains the maximum projection image of the second file. The second and third files each have 4 channels of data to compare image resolution: channel 1 - structured illumination, channel 2 - wide field, channel 3 - deconvolved wide field, and channel 4 - filtered deconvolved wide field. 

Images were collected with a Carl Zeiss SIM microscope using a 63 X 1.4 Plan Apo objective, an Andor Ixon camera with 150 ms exposures, Zeiss filter set 2, and a 488 nm laser.
DOI: 10.6075/j0db812z
title: CIL:18466, damselfly, flight muscle cell. In Cell Image Library

description: Most images show fractures through the outer membrane of mitochondria and SR/T tubules of dyads nestled in long grooves of the mitochondrial surface. All leaflets of the membranes appear in the images. This image is part of the group image CFA00512. TEM magnification 33900X. The negative film was scanned at LBL then reduced in size for upload. Scan step size is 6.3 micron, then reduced in size 4X for upload, for an effective pixel size of 25 micron. Technical details: Heads and tail removed, thorax bisected and immersed in 3% glutaraldehyde buffered in 0.1 M cacodylate buffer. pH 7.2. stored at 4C for several days. Muscle dissected out. Infiltrated in 30% glycerol in water. Frozen in liquid nitrogen cooled Freon, fractured in Balzers 400 Freeze-fracture, shadowed with platinum at 45o angle. Replicas were cleaned with Clorox (to remove tissue and with either sulfuric acid or NaOH to try removing the tracheolae. Replicas examined in a Philips 410 Microscope. Reference for these images: 
Takekura, H. and Franzini-Armstrong C. The structure of Ca2+ release units in arthropod body muscle indicates an indirect mechanism for excitation-contraction coupling. Biophys. J. 83, 83, 2742-2753, 2002.
description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: unembedded tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: digitized negative film
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j07h1hr7
title: CIL:9850, Paramecium tetraurelia, 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 antibody
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
Source of contrast: intrinsic mass distribution; stain with broad specificity
Visualization methods: stain with broad specificity; uranyl salt; gold
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed
description: Immunogold labeled microtubules next to the cytoproct radiate from basal bodies and also from the tip of the cytoproct. These microtubules lie along the approaching spent DV. b-tubulin immunogold labeled TEM image taken on 7/5/96 by R. Allen with Zeiss 10A operating at 80kV. Neg. 12,000X. Bar = 0.5µm. Cells were lightly fixed with 0.25% glutaraldehyde and infiltrated with 2.3M sucrose before being frozen in liquid nitrogen and thin sectioned at a temperature of –100°C at approximately 75nm thickness. Frozen sections from these preparations were then thawed, washed, and exposed to a monoclonal primary antibody that was raised in mice or rabbit/goat and to colloidal gold-complexed goat-anti-mouse/rabbit secondary antibodies. Further details of preparation are detailed in Methods Cell Biol. 2010;96:143-73. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. An unprocessed, high resolution version of this image (CIL:1307) is in the library and available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j09s1qkv
title: CIL: 52666, 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=6, y=2, z=11 from PS09_287383C_Myc_Terc
DOI: 10.6075/j0b56hwd
title: CIL:12594, Homo sapiens, squamous epithelial cell. In Cell Image Library

description: A human (Homo sapien) cheek cell smeared on a coverslip and imaged by birghtfield, phase contrast and differential interference contrast (DIC) microscopy. Images were acquired on a Zeiss Axiovert 200M microscope, with a Plan Apo 100x/1.4 Ph3 and a Plan Apo 100x/1.4 DICIII objective lens, equipped with a Photometrics CoolSnap HQ camera and operated by MetaMorph software. Scale bar represents 15 um.
description: Item type: recorded image
Imaging mode: bright-field microscopy; phase contrast microscopy; differential interference contrast microscopy
Parameter imaged: contrast-enhancing methods; optical path length gradient
Source of contrast: in-focus phase contrast; boundaries between regions with different refractive index
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j06w99qt
title: CIL: 53542, 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: 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.
DOI: 10.6075/j09s1q8t
title: CIL:1609, 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 0 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: 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
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.
DOI: 10.6075/j05m64vb
title: CIL:15005, Mus musculus, interneuron. In Cell Image Library

description: Distribution of interneurons expressing EGFP from the 5HT3 receptor promoter (Tg(Htr3a-EGFP)DH30Gsat, www.gensat.org) colabelled for calretinin in the cingulate cortex. A plexus of calretinin and EGFP positive axons can be seen in the superficial cortical layers. Many of the EGFP-expressing interneurons also express calretinin. 

Section (40 um) was imaged with a 32X, 0.4 NA Achroplan objective on a Zeiss Axiovert microscope. AF568 was excited at 562/40 nm and emission collected at 624/40 nm with Semrock filters and a single band dichroic (530-585 nm reflected, 601-800 nm transmitted). AF488 was excited at 482/35 nm and emission collected at 536/40 nm with Semrock filters and a single band dichroic (446-499 nm reflected, 513-735 nm transmitted). DAPI was excited at 350/50 nm and emission collected at 460/50 nm with a CLP400 dichroic (Chroma). Single images were captured for each channel using a Zeiss Axiocam MR CCD and pseudo-colored using Axiovision. See Davis and Puhl 2011 (Pubmed ID 21305052) for staining protocol. This image is part of a series characterizing EGFP expression from the 5HT3 promoter throughout the brain.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label; differences in adsorption or binding of stain; distribution of a specific protein
Visualization methods: 4',6-diamidino-2-phenylindole (DAPI); Alexa Fluor 568; EGFP
Data qualification: Raw
DOI: 10.6075/j0d50m27
title: CIL:15001, Mus musculus, CNS interneuron, hippocampal granule cell. In Cell Image Library

description: Distribution of interneurons expressing EGFP from the 5HT3 receptor promoter (Tg(Htr3a-EGFP)DH30Gsat, www.gensat.org) colabelled for somatostatin (red) and counterstained with DAPI (blue) to show the granule cell layer. EGFP-expression was amplified with chicken anti-GFP (Abcam, 1:2000). EGFP positive cells bodies and fibers are present throughout all layers of the hippocampus but enriched in the hilus (see associated images). Somatostatin expression is detected in a significant proportion of the EGFP-expressing interneurons in the hilus. Somatostatin immunoreactivity (Zymed rabbit polyclonal, 1:50) in the dentate gyrus identifies Hippocampal Interneurons of the Perforant Path (HIPP cells). HIPP cells project to the outer molecular layer of the dentate gyrus but also give rise to an axonal plexus within the hilus. See Tallent (2007) for more information on HIPP cells, Pubmed ID 17765724.

Section (40 um) was mounted with Fluoromount G and imaged with a 32X, 0.4 NA Achroplan objective on a Zeiss Axiovert microscope. AF568 was excited at 562/40 nm and emission collected at 624/40 nm with Semrock filters and a single band dichroic (530-585 nm reflected, 601-800 nm transmitted). AF488 was excited at 482/35 nm and emission collected at 536/40 nm with Semrock filters and a single band dichroic (446-499 nm reflected, 513-735 nm transmitted). DAPI was excited at 350/50 nm and emission collected at 460/50 nm with a CLP400 dichroic (Chroma). Single images were captured for each channel using a Zeiss Axiocam MR CCD and pseudo-colored using Axiovision. Background (linear) was subtracted from the image using Axiovision for presentation. See Davis and Puhl (2011), Pubmed ID 21305052, for a detailed staining protocol. This image is part of a series characterizing EGFP expression from the 5HT3 promoter throughout the brain.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label; differences in adsorption or binding of stain; distribution of a specific protein
Visualization methods: 4',6-diamidino-2-phenylindole (DAPI); Alexa Fluor 568; EGFP
Data qualification: Raw