cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j04x57mv
title: CIL:37030, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: This is IMAGE #9 (time point: 8 hour, rapid time lapse)of an image group. It is a projection of the time lapse series captured in IMAGE 8. It shows a neuron from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47. This time lapse series captures the dendritic arbor of this neuron every 60 seconds for 10 minutes. Over time, the tadpole (and the neuron) drifts across the field. In the series, z-stacks of this neuron were acquired at a 2 hour interval for 8 hours. Afterward, a second time lapse series was acquired at a 60 second interval for 10 minutes. This time series shows dendritic arbor development and morphological plasticity of the dendritic arbor with branch additions and retractions. The cell was transfected with in vivo electroporation of plasmid DNA encoding eGFP ~24 hours before the image was acquired. The intact, living tadpole was anesthetized, positioned under a glass coverslip and this image was taken directly through its transparent skin using a custom built two-photon microscope.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Specifications of the custom built two-photon microscope, including the laser sources, signal amplification, PMT specifications, and YFP filter sets are described in: 
Ruthazer ES, Li J, Cline HT. 2006. Stabilization of axon branch dynamics by synaptic maturation. J Neurosci 26(13):3594-3603. 

The methods of cell transfection with electroporation can be found here: 
Bestman JE, Ewald RC, Chiu S-L, Cline HT. 2006. In vivo single-cell electroporation for transfer of DNA and macromolecules. Nat Protocols 1(3):1267-1272. 

Further explanation can be found here:
Bestman JE, Cline HT. 2008. The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo. Proc Natl Acad Sci U S A 105(51):20494-20499.

Bestman JE, Cline HT. 2009. The Relationship between Dendritic Branch Dynamics and CPEB-Labeled RNP Granules Captured in Vivo. Front Neural Circuits 3:10.
DOI: 10.6075/j0d50n33
title: CIL:40134, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Tissue came from either mice genetically engineered to overexpress a mutant form of human alpha synuclein (A53T) (mouse strain, C57BL/6-DBA/2; group ID, A53T15+), or wild type animals from the same strain, anesthetized with nembutal, and perfused with 4% paraformaldehyde. Tissue was sectioned on a vibratome at a thickness of 80µm and immunostained with the following antibodies: mouse monoclonal anti-alpha-SYN; BD Transduction Laboratories, secondary conjugated to Alexa 488; rabbit polyclonal anti-mGluR5, Chemicon Ab. 5675, secondary conjugated to Rhodamine Red X. DAPI was dissolved in ProLong Mounting Medium and applied at the time of mounting. Section imaged using a Olympus Fluoview 1000, with a Olympus PlanApo 60X 1.4 NA objective.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody; Alexa Fluor 488; X-Rhodamine; 4',6-diamidino-2-phenylindole (DAPI)
Data qualification: Processed
description: The hippocampal area CA3 of a wildtype mouse immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei. This image has been downsampled from the raw data image, which can be accessed using the link provided to the Cell Centered Database. Other images in this group include transgenic mice engineered to overexpress a mutant form of human alpha synuclein (A53T), as well as examples from wild type specimens.
DOI: 10.6075/j0x34wkr
title: CIL:16233, Prochloron. In Cell Image Library

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: 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.
DOI: 10.6075/j0x34w6t
title: CIL:13384, Homo sapiens, mammary epithelia (MEC). In Cell Image Library

description: FISH detection of PTEN and VEGF gene loci in MCF-10.B2 cells during mammary epithelial differentiation and early mammary tumorigenesis. 
PTEN (red) and VEGF (green)were detected in paraformaldehyde fixed MCF10A.B2 cells grown for 20 days under 3D growth conditions. DAPI (blue) delineates nuclei. A representative acinus structure is shown. The z-series was recorded with a Zeiss LSM 510 META confocal microscope with a 63x 1.4 NA objective lens and zoom level 3. Optical sections imaged totaled approximately 15-20 microns in thickness.
See Fig 2 in Meaburn and Misteli, 2008 J Cell Biol 180:39-50.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Fluorescein (FITC); 4',6-diamidino-2-phenylindole (DAPI); Rhodamine
Processing history: unprocessed raw data
DOI: 10.6075/j04f1qkv
title: CIL: 54633, Mus musculus, oocyte. In Cell Image Library

description: FIG. 3Dt, 3Deq Maturation of cortical ER clusters during different stages of fertilization.
description: Imaging mode: whole mount confocal image
Visualization methods: Laser Scan Confocal; PMT
description: Oocytes fixed with 2% paraformaldehyde and 1% picric acid. Immunolabelled with anti-Calreticulin (green), Alexafluor 568-phalloidin (red), and Hoechst 33342 (blue).
DOI: 10.6075/j07p8xg0
title: CIL:21778, Drosophila melanogaster, epithelial. In Cell Image Library

description: Five different samples of Drosophila melanogaster Kc167 cells were stained with Hoechst 33342, a DNA stain. The last sample (labeled nodsRNA, CIL 21789) is of wild-type cells. Each of the other four samples (labeled 48, 340, Anillin, and mad2, CIL 21749, 21739, 21759, and 21773, respectively) has a different gene knocked down by RNAi. This is the set that were treated with mad2 RNAi. There are 10 images of each sample, for a total of 50 images. The images were acquired on a Zeiss Axiovert 200M microscope. A recommended use for these five image sets is to algorithmically compute the number of cells in each image. A tab-delimited text file containing this information can be found at the URL indicated in the attribution box. The recommended citation when using these images is: "We used the Drosophila Kc167 1 image set (Carpenter, et al., Genome Biology, 2006) available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
description: Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of DNA
Visualization methods: Hoechst 33342
Processing history: unprocessed raw data
DOI: 10.6075/j05m65gt
title: CIL: 54212, Homo sapiens, HeLa. In Cell Image Library

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.
description: Visualization methods: confocal microscopy
DOI: 10.6075/j04t6j36
title: CIL: 54481, Homo sapiens, astrocyte. In Cell Image Library

description: 5 um sections of FFPE prefrontal cortex tissue from post-mortem, human Alzheimer's disease donor labeled for glial fibrillary acidic protein (GFAP), a protein commonly used to identify astrocytes.
description: Imaging mode: bright-field microscopy
Visualization methods: GFAP IHC using HRP/DAB
description: Pathology load assessment of de-identified, human, post-mortem Alzheimer's disease and age-matched non-symptomatic donor prefrontal cortex brain tissue. We used these imaging data to inform donor stratification when we generated a large single nuclei RNA sequencing (snRNA-seq) dataset. Given we generated both imaging and snRNA-seq datasets the same location/piece of tissue for each donor, this gives us an unprecedented platform to evaluate cell type/subpopulation transcriptomes and relate them directly to their respective tissue microenvironments.
DOI: 10.15468/dl.7u9pjf
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Caragana acanthophylla"
 ]
}

 The dataset includes 46 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009619-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17463634
title: Dataset on xenon-133 atmospheric background source distribution variables for graph modelling

description: This dataset supports the findings of our manuscript entitled «A Graph Signal Processing Approach to the Characterization of Xe-133 Atmospheric Background» and is provided to enable reproducibility. Characterizing the global xenon-133 atmospheric background is essential in the context of the Nuclear-Test-Ban Treaty. In this original study, we address this problem using a graph model that represents relationships between stations of the IMS network. Using simulated data where the contributions of each source are known, we investigate how source distributions shape the background field. Spectral clustering reveals that the stations can be grouped into distinct regions according to their source distributions. Furthermore, we use the graph model to estimate sources from the aggregated xenon-133 concentrations at each station, showing good performance on our simulations and providing insight into source-station relationships. Our graphs are built using variables provided in this dataset, through a process detailed in the "Methods" section of the manuscript.
DOI: 10.5281/zenodo.17463635
title: Dataset on xenon-133 atmospheric background source distribution variables for graph modelling

description: This dataset supports the findings of our manuscript entitled «A Graph Signal Processing Approach to the Characterization of Xe-133 Atmospheric Background» and is provided to enable reproducibility. Characterizing the global xenon-133 atmospheric background is essential in the context of the Nuclear-Test-Ban Treaty. In this original study, we address this problem using a graph model that represents relationships between stations of the IMS network. Using simulated data where the contributions of each source are known, we investigate how source distributions shape the background field. Spectral clustering reveals that the stations can be grouped into distinct regions according to their source distributions. Furthermore, we use the graph model to estimate sources from the aggregated xenon-133 concentrations at each station, showing good performance on our simulations and providing insight into source-station relationships. Our graphs are built using variables provided in this dataset, through a process detailed in the "Methods" section of the manuscript.
DOI: 10.6075/j0k64gx6
title: CIL:39044, Aggregatibacter actinomycetemcomitans, Gram-negative bacteria. In Cell Image Library

description: Colorized light micrograph of Aggregatibacter actinomycetemcomitans colonies. A. actinomycetemcomitans is a Gram-negative bacteria commonly found to cause infections of the oral cavity and often isolated from the periodontal pocket. The peridontium refers to the soft tissue that surrounds and supports the teeth. Related images available as CIL:39042, 39045, and 39046.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: modes of light microscopy
Parameter imaged: absorption of illumination
Source of contrast: differences in amount of elastic light scattering
Visualization methods: visualization of contiguous regions
Processing history: colorized
description: B0007676 Colonies of A. actinomycetemcomitans. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
DOI: 10.6075/j06d5stm
title: CIL:36834, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Specifications of the custom built two-photon microscope, including the laser sources, signal amplification, PMT specifications, and YFP filter sets are described in: 
Ruthazer ES, Li J, Cline HT. 2006. Stabilization of axon branch dynamics by synaptic maturation. J Neurosci 26(13):3594-3603. 

The methods of cell transfection with electroporation can be found here: 
Bestman JE, Ewald RC, Chiu S-L, Cline HT. 2006. In vivo single-cell electroporation for transfer of DNA and macromolecules. Nat Protocols 1(3):1267-1272. 

Further explanation can be found here:
Bestman JE, Cline HT. 2008. The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo. Proc Natl Acad Sci U S A 105(51):20494-20499.

Bestman JE, Cline HT. 2009. The Relationship between Dendritic Branch Dynamics and CPEB-Labeled RNP Granules Captured in Vivo. Front Neural Circuits 3:10.
description: This is IMAGE #4 (day 2) of a time lapse series contained with in this image group. It shows the dendritic arbor of a neuron from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47. Autofluorescent pigment cells are visible in the superficial layers of the z-stack. 
 
 The images were acquired daily over 2 days and show dendritic arbor development and morphological plasticity of the dendritic arbor with branch additions and retractions.
 
 The cell was transfected with in vivo electroporation of plasmid DNA encoding eYFP ~24 hours before the first image was acquired. The intact, living tadpole was anesthetized, positioned under a glass coverslip and this image was taken directly through its transparent skin using a custom built two-photon microscope.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EYFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j04q7ssd
title: CIL:26548, Mus musculus, fibroblast. 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
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: Alexa Fluor 488; Alexa Fluor 546
Data qualification: Raw
description: Cells were cultured in DME (Invitrogen) supplemented with 10% fetal bovine serum and 100 U/ml penicillin/streptomycin (Invitrogen) at 37°C in a humidified 5% CO2 incubator. Scrambled blebbistatin for 30 min, and co-stained for betaPIX (green) and actin (rhodamine phalloidin). Images were captured by Olympus IX81-ZDC inverted microscope with UPlanFL N 40X objective.
description: To study the molecular mechanism by which nonmuscle myosin II (MII) regulates protrusion and adhesion dynamics in migrating cells, NIH3T3 cells were treated with βPIX siRNA for 2 days, treated with blebbistatin (BBS) for 30 min., and stained for βPIX (green) and actin (red). These findings help elucidate a functional link between MII and Rac1/Cdc42 GTPases, which may regulate protrusion/adhesion dynamics in migrating cells. This image is the original data file from Fig. 6B, “Requirement for βPIX in MII-regulated cell protrusion and adhesion.” J. Cell Biol. 2010. Vol. 190(4):663–674.
DOI: 10.15468/dl.4eapw8
title: Occurrence Download

description: A dataset containing 136 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Atraphaxis spinosa"
 ]
}

 The dataset includes 136 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009621-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0zs2v5d
title: CIL:13732, Homo sapiens, endothelial cell. 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: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EYFP; primary antibody plus labeled secondary antibody
Processing history: brightness and contrast adjusted
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Mitochondria in HeLa cells are identified by mito-YFP (green) following treatment with the mitochondrial depolarizing agent CCCP (carbonyl cyanide m-chlorophenyl hydrazone). When fixed cells are permeabilized with 0.25% Triton X-100 (TX-100), both antibodies to cyctochrome c (red), a mitochondrial matrix marker, and the antibody to Tom20 (white), a mitochondrial outer membrane marker, are able to bind their epitopes. Mito-YFP transfected HeLa cells were treated with DMSO for 3 hrs, fixed with 4% paraformaldehyde and permeabilized with 0.25% Triton X-100/PBS. Primary antibodies used were: anti-Cyt c mAb (BD) and anti-Tom20 mAb (BD); secondary antibodies used were: Alexa Fluor 594 and 647. Imaging was performed on an LSM510 Meta (Carl Zeiss, Inc) with a 63x 1.4 NA oil differential interference contrast Plan Apo objective. Image contrast and brightness were adjusted in the LSM image browser (Zeiss). This image corresponds to Fig 4b, bottom row and is part of a differential permeabilization assay with and without CCCP that is further described in Fig 4b of J Cell Biol, 191: 933-942, 2010. Images in Fig 4 include CIL#s 13733, 13734, 13729, 13730, 13731, 13732, 13717, 13718, 13719, 13720, 13721, 13722, 13723, 13724.
DOI: 10.6075/j03n22xm
title: CIL: 52596. In Cell Image Library

description: One z layer of a z-stack at the given tile position
description: Tile x=2, y=1, z=4 from PS09_20676_2B_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
DOI: 10.6075/j0mg7nxg
title: CIL: 50704, FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles. In Cell Image Library

description: FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles. Postnatal day 4 mouse Inner Ear Organ of Corti labeled with anti-PKHD1L1 antibody (10 nm gold beads). The dataset represents the apical end of the Outer Hair Cell with the stereocilium bundle. Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample.
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: Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample. 
4.1_Cell_4_Raw_Image_Stack_Part1 is a multipage TIFF file consisting of 224 individual EM sections acquired at 15 nm milling step, resulting in 1.95×1.95×15 nm³ voxel size. 
This file is a part of Dataset 4, comprised of files related to the Cell #4. The numbering order of the files reflects the order of operations performed during the analysis. Note: The data acquisition session was interrupted after frame #224, and later resumed as a separate imaging session. This resulted in two stack files, concatenated into a single multipage TIFF file during data analysis.