cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j00r9p32
title: CIL: 54045, 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: 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.
DOI: 10.6075/j0rx9c67
title: CIL:40229, Mus musculus, Purkinje cell. In Cell Image Library

description: Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: intracellular filling
Visualization methods: lucifer yellow
Data qualification: Processed
description: Tissue was perfused with paraformaldehyde, sectioned (100 µm) on a vibratome and mounted in gelvatol, and imaged on a Biorad Radiance 2000 Confocal using a 60x 1.4NA objective.
description: A Purkinje neuron from the cerebellum of a 2 month old male C57BL/6 mouse, injected with Lucifer Yellow. The elaborate, highly branched dendritic arbor is revealed in this maximum projection image which was generated by compiling a z-series of optical sections. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
DOI: 10.6075/j0r49qvz
title: CIL:35801, Saccharomyces cerevisiae. In Cell Image 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: A time lapse experiment of Saccharomyces cerevisiae expressing GFP-tagged MCM1. 
 
 MCM1 is a transcription factor involved in cell-type-specific transcription and pheromone response; plays a central role in the formation of both repressor and activator complexes
 
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: 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/j04748zg
title: CIL:7112, Homo sapiens, neuron. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: microscopy; atomic force microscopy
Parameter imaged: specimen height
Source of contrast: specimen height
Processing history: unprocessed raw data
description: The protein MeCP2 binds to symmetrically methylated CpG dinucleotides and is thought to transmit the (generally) repressive signals encoded in DNA methylation patterns. Mutations in MeCP2 lead to Rett syndrome. Here, MeCP2-DNA complexes have been imaged by AFM (Digital Instruments Nanoscope) in air using human MeCP2 and an 828 bp DNA sequence containing several methylated CpGs. MeCP2 molecules appear as bright particles in AFM images. Volume measurements of the complexes suggest that MeCP2 monomers (circular particles) and dimers (larger elliptical particles) are present and suggest that MeCP2 binds DNA cooperatively. Other images in the grouped set show looped structures and large complexes containing multiple DNA strands and MeCP2 molecules. These configurations are likely promoted by the multiple independent DNA-binding domains of MeCP2 and relevant to the in vivo interactions between MeCP2 and chromatin.
DOI: 10.6075/j00z7285
title: CIL:35647, Saccharomyces cerevisiae. In Cell Image 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
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
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 Cdc20, a cell-cycle regulated activator of anaphase-promoting complex/cyclosome (APC/C) required for metaphase/anaphase transition; directs ubiquitination of mitotic cyclins, Pds1p, and other anaphase inhibitors; potential Cdc28p substrate novel protein thought to be involved in cell cycle regulation.These phase,gfp images are part of an image group that ranges from CIL:35640-35659. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the Library.
DOI: 10.6075/j0348jxh
title: CIL: 52690, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Tile x=3, y=4, z=14 from PS11_10021_2B_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/j0gx49sn
title: CIL:814, Homo sapiens, permanent cell line cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; glycerol permeabilized; detergent permeabilized; primary antibody plus labeled secondary antibody
Relation to intact cell: whole mounted tissue
Item type: microscopy
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: local accumulation of fluorescent probe
Visualization methods: Rhodamine
Processing history: unprocessed raw data
description: This culture of HeLa cells was grown, fixed and labeled directly on 35-mm plastic petri dishes (not on cover slips). To preserve the 3D structure of cells, cultures were fixed in formaldehyde vapors at room temperature over 20 min. Fixation was performed as follows: medium was completely aspirated, a 50ul drop of 37% formaldehyde was placed on the lid of the dish and covered with the dish of cells, bottom up. After fixation dishes were carefully filled with 1ml of 50% glycerol in PBS and dishes were stored at -20 C until staining. 

Before staining, cells were incubated with blocking solution (5% fetal calf serum, PBS, 0.2% triton x-100, 25 min room temp.), then treated with primary antibody, which was mouse anti-Cytochrome C from BD Pharmigen (cat.# 556433) diluted 1:100 in blocking solution, 1h room temp. After standard washing (PBS 3-4 times, 5 min each), secondary antibody (donkey monovalent Fab-fragment anti-mouse IgG conjugated with Rhodamine Red-X from Jackson ImmunoResearch laboratories, concentration 2.5ug/ml) was applied.

Images were captured on a Zeiss Axioplan-2. Objective - 63x oil immersion/NA 1.25. Magnifying lens (optovar) was 1.5. Digital camera – Hamamatsu ORCA-ER. Program – AxioVision 3.5.1. Illumination-mercury bulb HBP50. Filter set – standard for Rhodamine/Cy3/Alexa 564 – excitation 530-585 and emission LP 615. Mounting medium-VectaShield.
DOI: 10.6075/j0qf8s6p
title: CIL:2227, 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 6 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: 10.15468/dl.bn62r7
title: Occurrence Download

description: A dataset containing 50 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Centaurea adpressa"
 ]
}

 The dataset includes 50 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009647-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dnh5tx
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Hypericum scabrum"
 ]
}

 The dataset includes 19 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009646-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0m32vhw
title: CIL: 54352, Homo sapiens, HeLa. In Cell Image Library

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.
description: Visualization methods: confocal microscopy
DOI: 10.6075/j0kw5fx2
title: CIL: 54762, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Epifluorescent imaging
description: Imaging mode: fluorescence microscopy
Visualization methods: epifluorescent imaging
description: Nanog staining
DOI: 10.6075/j0sq9007
title: CIL: 53083, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given image
description: Image 1, z=8 from SC_030
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/j0db813d
title: CIL:2215, Caenorhabditis elegans. In Cell Image Library

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
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 6 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.
DOI: 10.6075/j0m32v3h
title: CIL:39787, Lytechinus pictus, mesenchymal cell. In Cell Image Library

description: Scanning electron microscope image of Strongylocentrotus drobachiensus [sea urchin] at the gastrula stage. Embryo was split open to reveal the blastocoel cavity. There are several migrating mesenchyme cells, with a variety of filopodial shapes.This image is part of a group of SEM images of sea urchin embryos at various stages of development. The group is available as CIL:39782-39791.
description: Images taken on a JEOL 35C SEM. 
Processing protocol:
1. 2% GTA in 75% MBL SW or FilteredSW 
FSW - fix for 1.5hrs. RT.
2. Rinse with 0.1M NaCacodylate buffer pH 7.4
3. 0.5% OSO4 in .075M NaCacodylate buffer pH 7.4 - 30' in the cold
4. Rinse in 0.1M NaCacodylate buffer ph 7.4
5. Dehydrate thru ETOH: 30%, 50%, 70%, 95% for 5 min each
6. 100% - 3 changes - 15' each
7. Critical Point Dry
8. Stick embryos down onto silver paint. Gently crack open with glass needle (pipette drawn out to a fine point).
9. Sputter coat with AuPd.
description: Preparation: glutaraldehyde fixed tissue; critical_point dried specimen; ethanol dehydration
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; visualization of contiguous regions; osmium tetroxide
Processing history: unprocessed raw data
DOI: 10.6075/j0fq9w4p
title: CIL: 52242, Mus musculus, Retinal Pigment Epithelial cells. In Cell Image Library

description: Imaging mode: confocal microscopy
Visualization methods: primary antibody plus labeled secondary antibody
description: Merged confocal image of mouse (C57BL/6J, postnatal day 180) retinal pigment epithelium (RPE) flatmount. The image is stained for ZO-1 (Green, tight junctions between cells) and nucleus (Red, Propidium Iodide). The RPE cells are in general regularly shaped and arranged polygonal cells, however, their shape and arrangement changes significantly according to their location and age.
description: Mouse eye was enucleated, fixed for 10 min in 10% neutral buffered formalin, and washed three times with PBS. Flatmounting was done by making four radial cuts from the center of the cornea back toward the optic nerve. The iris and retina were removed using forceps and additional incisions were made at the ciliary body/cornea margin to relieve tension from the sclera. The RPE flatmounts were stained for rabbit anti-ZO1 antibody (1:100 dilution, catalog no. 61-7300; Invitrogen, Carlsbad, CA) and goat anti-rabbit IgG secondary antibody (catalog no. O11038; Invitrogen). Imaging of the flatmounts was performed with a confocal imaging system (model C1; Nikon) using argon laser excitation at 488 nm. Confocal images were digitally merged (Adobe Photoshop CS2; Adobe, San Jose, CA).
DOI: 10.6075/j0862fr0
title: CIL:1748, Caenorhabditis elegans. In Cell Image Library

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
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 2 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.
DOI: 10.6075/j0513xsz
title: CIL: 52880, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Tile x=4, y=5, z=15 from PS11_167511L_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/j0222t3s
title: CIL:39775, Mus musculus, cardiac muscle cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; formaldehyde fixed tissue; tissue in epoxy resin embedment; ethanol dehydration
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
Visualization methods: uranyl salt; lead salt
Processing history: unprocessed raw data
description: Primary fixation included: 2.5 % glutaraldehyde, 2% formaldehyde in 0.1 M Na-phosphate buffer, pH 7.4. Post-fixed in 2% OSO4 in 0.1 M Na-phosphate buffer, pH 7.4. Stained en bloc in 1% uranyl acetate. The tissue was then dehydrated in a graded series of ethanol and infiltrated with Spurr's resin. Thin sections of 70 nm were trimmed using a diamond knife and post-stained in uranyl acetate and lead citrate. This micrograph image was taken using a Phillips CM 100 transmission electron microscope at an accelerating voltage of 80kV.
description: Transmission electron micrograph showing adjacent muscle fibers from the ventricle of a mouse cardiac muscle. This image shows the organization of muscle tissue, nucleus, cell walls and blood vessels.
DOI: 10.34810/data920
title: Assesment of technical green-roof indicators: database application
title: Project Verd de Proximitat BCN

description: This dataset contains a web application (written in Flask, Python) to register periodic and one-time data that is later used to assess technical indicators for the performance of green roofs. All entires are automatically added to an SQLite database. In its presented form, six green roofs of Barcelona are included, but this can be customised as wished.

An empty database file is provided along with the SQLite schema to generate the tables. The Python code is also included in order to allow the application to be offered through a server.

The application registers one-time, yearly and monthly data needed for the assessment of green roofs. The menu is offered in English.
description: The application is written in Flask (Python) and needs to be run on a Linux/BSD server. Once on a server, the application runs in any browser. 

The resulting database is a sigle SQLite file that can be edited and processed with any SQLite application, like DB Browser for SQLite.
DOI: 10.6075/j07s7mjt
title: CIL:13698, Chlorocebus aethiops. In Cell Image Library

description: Preparation: crosslinking-fixative fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: Alexa Fluor 488; TexasRed
Data qualification: Processed
description: This is one of a group of four images in Figure S5 in Apaja et al., JCB 2010, that support the conclusion that the WT vasopressin type2 receptor (V2R) and the V2R W164S mutant (that causes nephrogenic diabetes insipidus) have different post-endocytic targeting. The sorting of endocytosed myc-tagged WT and W164S V2R was determined by indirect immunolabeling of internalized receptors in transiently transfected COS7 cells. The WT and temperature (26 degrees C) rescued mutant receptors were labelled with anti-myc Ab in live cells (1h) and then chased in Ab-free medium (1h, 37 degrees C) before indirect immunolabeling. To mark lysosomes, cells were labeled with 10 kD Texas red–dextran at 50 µg/ml by overnight fluid-phase endocytosis and chased for &gt;3 h at 37°C. Fluorescence micrographs were obtained by a microscope (LSM510 or LSM710; Carl Zeiss, Inc.) equipped with a Plan-Apochromat 63×/NA 1.4 objective in multitrack mode. This single optical section shows that the internalized W164S V2R mutant co-localizes with lysosomes. A companion image in this group shows that WT V2R, however, does not co-localize with lysosomes.