cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0j38rjr
title: CIL:7339, Opercularia [NCBITaxon:168247], Opercularia coarctata, cell by organism, eukaryotic cell, Eukayotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
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: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: High resolution image of elements of myonemal fibers which lie next to the epiplasm that lies internal to the plasma membrane and alveoli. A close association of the ER with the myonemes is seen. The cytosol is filled with ribosomes, peroxisomes, and mitochondria. The ER next to the oral region provides a site for formation of elements of the Golgi complex. TEM taken on 6/11/69 by R. Allen with Philips 300 operating at 60KV. Neg. 14,800X. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis.

Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness.

Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0pv6k11
title: CIL: 53758. In Cell Image Library

description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
description: CMGC family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
description: Visualization methods: confocal microscopy
DOI: 10.6075/j0br8qxz
title: CIL:13891, Saccharomyces cerevisiae. In Cell Image Library

description: 3HA-Bfa1 (red) is now symmetrically localized to both spindle pole bodies (SPB) in cells with constitutive targeting of Tem1 to both SPBs in metaphase as determined by spindle morphology (tubulin, green) and nuclear morphology (DAPI, blue). Compare to control image CIL# 13890. Image is Fig 4C, bottom panels, in J Cell Biol. (2011) 192: 599-614. Images in Fig 4 include CIL# 13890, 13891, 13892, 13893.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: widefield illumination; fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; compartmentalization of stain or label
Visualization methods: HA peptide tag; 4',6-diamidino-2-phenylindole (DAPI); primary antibody plus labeled secondary antibody; Cy3; Fluorescein (FITC)
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Cells (MATa tem1::KanMX ura3::eGFP-CNM67–TEM1::URA3 bfa1::3HA-BFA1) grown in rich media with glucose were fixed for 15 min in 3.7% formaldehyde and 0.1 M potassium phosphate buffer, pH 6.4. Cells were then washed twice with 0.1 M potassium phosphate buffer, pH 6.4, and resuspended in 1.2 M sorbitol in 0.12 M K2HPO4/0.033 M citric acid, pH 5.9. Fixed cells were digested with 0.1 mg/ml zymolyase-100T (US Biological) and 1/10 volume of glusulase (PerkinElmer) at 30C for 15 min, washed once, and resuspended in 1.2 M sorbitol in 0.12 M K2HPO4/0.033 M citric acid, pH 5.9. Primary antibodies were anti-HA monoclonal antibody (HA.11; 1:500) and anti-tubulin (Abcam; 1:500). Secondary antibodies were: anti-mouse Cy3 (for HA) and anti-rat FITC (for tubulin). Cells were resuspended in DAPI (1 mg/ml). Imaging was performed at 25C using a Leica DM6000 microscope equipped with a 100x/1.40 NA oil immersion objective lens, A4, L5, and TX2 filters, and a digital CCD camera (DFC350, Leica). Pictures were processed with LAS AF (leica) and ImageJ software.
DOI: 10.6075/j0n58k8q
title: CIL:36652, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: QF-DE of the separation spindle of a micronucleus apparently near a daughter micronucleus (not in section plane). The spindle is filled with microtubules linked together by bridges or by motor proteins. An intact nuclear envelope with pores encloses the spindle. TEM taken on 5/12/91 by R. Allen with Zeiss 10A operating at 80kV. Neg. 19,800X. Bar = 0.25µm.
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; Print of negative scanned for Photoshop
Data qualification: Processed
DOI: 10.6075/j02r3qw4
title: CIL:1671, 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: 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
DOI: 10.6075/j02j6c0d
title: CIL:48011, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

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
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.
DOI: 10.6075/j0wm1dkp
title: CIL:50674, Drosophila melanogaster. In Cell Image Library

description: We show in this study that brain and intestinal stem cells of Drosophila contain a new type of cytoplasmic protrusion which is enriched in mitochondria and that the mitochondria are probably dependent on microtubules for their distribution. The protrusions form mitochondria-enriched cytoplasmic bridges from the stem cells to their niche that we speculate are important in regulating stem cell quiescence and activation.
description: Specimen preparation: Larval brains (LBs) were prepared from starved (amino acid-restricted) first instar (L1) larvae to enrich for quiescent neural stem cells. The LBs were glutaraldehyde-fixed, tannic acid and OsO4-stained, embedded in resin, thin-sectioned (60-70 nm) and stained with uranyl acetate/lead citrate, then observed by TEM.
description: Item type: Digital
Imaging mode: CM12 TEM equipped with AMT digital camera
DOI: 10.6075/j0tq61nb
title: CIL:36356, Rattus norvegicus, astrocyte, astrocyte of the hippocampus. In Cell Image Library

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: intracellular filling
Visualization methods: lucifer yellow
Data qualification: Processed;spatialmeasurements
description: Male Sprague Dawley rats, 4 weeks of age, were anesthetized and perfused transcardially with with Ringer's solution (37°C), followed by 4% paraformaldehyde (PFA) in PBS (37°C, pH 7.4). Tissue was sectioned (100 µm thick) using a vibratome, and injected with a BX50WI microscope (Olympus, Melville, NY) and, using infrared differential interference contrast videomicroscopy, cells with a small diameter soma (approx. 7–11µm) in the stratum
radiatum of CA1 were located and impaled with glass micropipettes filled with 5% aq. Lucifer Yellow. The astrocytes were filled using 0.5 Hz pulses of current until all of the processes were brightly fluorescent. After several astrocytes were filled, a slice was placed in the 4% PFA overnight at 4°C. Slices were then imaged after coverslipping in Gelvatol. Confocal images were acquired with a BioRad Radiance2000 (Hercules, CA) attached to a Nikon E600FN (Kanagawa, Japan) microscope equipped with a Nikon (Tokyo, Japan) 60x oil objective (NA 1.4). Additional details are provided in Bushong EA, Martone ME, Ellisman MH. Maturation of astrocyte morphology and the establishment of astrocyte domains during postnatal hippocampal development. Int J Dev Neurosci. 2004 Apr;22(2):73-86.
description: Intracellular dye injections of protoplasmic astrocytes from the CA1 region of hippocampus of a 4 week old rat reveals highly ramified spongiform processes. Astrocytes were filled with Lucifer Yellow. Optical sections were generated with a single photon confocal microscope, and compiled here as a single maximum projection image. 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/j0th8m0j
title: CIL:2171, 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 4 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/j0gx49nv
title: CIL:2635, Caenorhabditis elegans. In Cell Image Library

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 12 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: 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/j0gm8683
title: CIL:27221, Homo sapiens, blood cell, red blood cell. In Cell Image Library

description: This image set consists of five differential interference contrast (DIC) images of red bood cells (approximately 8 microns in diameter). Each image in the set contains a DIC image and a thresholded image. There are two options when using this data set to quantify an algorithm's effectiveness. The simplest method is simply to compute the percentage of pixels that your algorithm and the thresholded image have in common. However, a wide class of algorithms for handling DIC images do not explicity segment the image, but rather transform the image so that it can later be thresholded. These images were obtained from http://www.broadinstitute.org/bbbc/human_rbc_dic.html

DIC images attributed to Skerker, Rush, and Wiegand; the thresholded images attributed to Morgan.
description: Preparation: dispersed cells
Relation to intact cell: whole mounted cells
Item type: recorded image; threshold image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: differences in intrinsic optical density
Visualization methods: visualization of contiguous regions
Processing history: threshold
DOI: 10.6075/j0hh6j22
title: CIL:35649, 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/j0319w37
title: CIL: 54850, Danio rerio, Whole larva. In Cell Image Library

description: Imaging mode: SBEM
description: Transverse sections of 5 days post-fertilization wild-type zebrafish larva in the region of the anterior kidney.
description: Brief description of sample preparation and SBEM imaging

5 d.p.f. zebrafish larva was prepared for SBEM. Larva was fixed in 2.5% glutaraldehyde and 4% paraformaldehyde in 0.15 M cacodylate buffer (CB, pH 7.4) at 4°C overnight. After removing the fixative, larva was treated for 15 minutes with 20 mM glycine in 0.15M CB, on ice to quench the unreacted glutaraldehyde. Then, larva was washed with 0.15 M CB and then placed into 2% OsO4/1.5% potassium ferrocyanide in 0.15 M CB containing 2 mM CaCl2. The larva was left for 30 min on ice and then 30 min at room temperature (RT). After thorough washing in double distilled water (ddH2O), larva was placed into 0.05% thiocarbohydrazide for 30 min. Larva was again washed and then stained with 2% aqueous OsO4 for 30 min. Larva was washed and then placed into 2% aqueous uranyl acetate overnight at 4°C. Larva was washed with ddH2O at RT and then stained with 0.05% en bloc lead aspartate for 30 min at 60°C. Larva was washed with ddH2O and then dehydrated on ice in 50%, 70%, 90%, 100%, 100% ethanol solutions for 10 min at each step. Larva was then washed twice with dry acetone and placed into 50:50 Durcupan ACM:acetone overnight. Larva was transferred to 100% Durcupan resin overnight. Larva was then flat embedded between glass slides coated with mould-release compound and left in an oven at 60°C for 72 h. The larva block was a Zeiss Gemini scanning electron microscope equipped with a Gatan 3View2XP and OnPoint backscatter detector. Images were acquired at 4.0 kV accelerating voltage with a 30 μm condenser aperture and 0.5 μsec dwell time; Z step size was 70 nm; pixel size was 9.5 nm; raster size was 25k x 12k, variable pressure under nitrogen. The volume was aligned using cross correlation, segmented, and visualized using IMOD.
DOI: 10.6075/j0348kd6
title: CIL:10361, Rattus, multipolar neuron. In Cell Image Library

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

Detailed methods: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained for MAP2 (HM2, from Sigma with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 40X lens (HCX PL Fluotar, NA 0.75), Photometrics CoolSnap ES CCD camera and MetaMorph software. A multilayer stack of the fluorescent image of MAP2 staining and the phase image was generated using MetaMorph.
DOI: 10.6075/j0ws8sft
title: CIL:10274, Halteria grandinella, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
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: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; Print scanned for Photoshop
Data qualification: Processed;spatialmeasurements
description: An image of the microtubular nemadesmata that extend deep into the cytosol from the membranelles of the perioral kinetids. Bridges link the plasma membrane to the alveoli. Parasomal sacs occur around the basal bodies and a nascent food vacuole is evident. TEM taken on 3/18/71 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 13,750X. The negative was printed to paper and the image was scanned with a flatbed scanner and the 0.5µm bar added in Photoshop. This digitized image is available for qualitative analysis. A raw, unprocessed, high resolution version of this image (CIL:7619) is in the library and available for quantitative analysis. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.15468/dl.8md32d
title: Occurrence Download

description: A dataset containing 44235 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Acer pictum, Betula platyphylla, Juglans mandshurica, Populus davidiana, Fraxinus mandshurica, Quercus mongolica, Ulmus davidiana, Castanopsis fissa, Machilus chinensis, Schima superba, Triadica cochinchinensis, Cryptocarya chinensis, Gironniera subaequalis, Psychotria asiatica, Pterospermum heterophyllum)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "EventDate is greater than or equal to 1991-01-01",
 "EventDate is less than or equal to 2025-10-31",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than or equal to 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 44235 records from 242 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009406-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.