cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j03x85d5
title: CIL:26317, Saccharomyces cerevisiae. In Cell Image Library

description: Preparation: high pressure freezing; freeze substitution
Relation to intact cell: microtome-sectioned tissue
Item type: portrayed image
Imaging mode: transmission electron microscopy (TEM); tilt series; tomogram
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: surface rendering; volume rendering
description: Endoplasmic reticulum (ER) domains in 3D in a wild type S. cerevisiae cell (mutant = NDY257) with a 596-nm bud. Domains are color coded as follows: Golgi (purple), and vesicles (30 nm is shown in pink, and 60 nm is shown in white), NE (orange), pmaER, cecER, tubER (pink), and blue shade is the PM. Haploid cells were high pressure frozen and then freeze substituted with 0.1% uranyl acetate and 0.25% glutaraldehyde in anhydrous acetone, embedded in Lowicryl, and an 80-nm serial thin sections and 200-nm serial semithick sections were cut with an ultramicrotome. Dual-axis tilt series were collected from the samples from +/-60° with 1° increments at 300 kV using SerialEM (Mastronarde, 1997) at 300 kV using a field emission gun (Tecnai 30; FEI). Tilt series were recorded at a magnification of 23,000× using SerialEM (Mastronarde, 2005). After 2x binning on the recording 4098 x 4098–pixel charge-coupled device camera (Megascan 795; Gatan, Inc.), this magnification creates a 2000 x 2000–pixel image with a pixel size of 1.02 nm on the specimen. The nominal resolution in our tomograms was ~4 nm, based upon section thickness, number of tilts, tilt increments, and tilt angle range (Crowther relation; Koster et al., 1997). The IMOD package (Kremer et al., 1996) and its newest viewer, 3DMOD 4.0.11, were used to construct individual tomograms. Videos were made in 3DMOD and assembled in QuickTime Pro 7. Bar is 200 nm. Video relates to Figure 4 and Video 7 of J Cell Biol 2011 193:333-346.
DOI: 10.6075/j0zk5fvg
title: CIL:10711, Notophthalmus viridescens, oocyte. In Cell Image Library

description: Meiotic newt oocyte nuclei were allowed to disperse in 30 mM KCl/NaCl, centrifuged through 2% formaldehyde onto an EM grid, stained with uranyl acetate, and critical point dried. Grids were examined with the Madison 1MeV TEM at 10 KX. This micrograph, showing transcription on looped lampbrush chromosomes was recorded at a tilt angle of 55 degrees. The image is grouped with one of the same sample area recorded at a 45 degree tilt. A stereo examination of the pair provides an oblique 3D view.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: transmission electron microscopy (TEM)
Imaging mode: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
DOI: 10.6075/j0h13229
title: CIL:32105, Homo sapiens, osteocarcenoma. In Cell Image Library

description: The images constitute one row of a 348 well plate. The dose curve consists of 11 dose points and one control. Each concentration is duplicated in adjacent wells. Each well has three fields.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: plate reader
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; distribution of DNA
Visualization methods: EGFP
Processing history: unprocessed raw data
description: This image set is of Transfluor assay where an orphan GPCR (G-protein coupled receptor) is stably integrated into a beta-arrestin GFP (green) expressing U2OS cell line also showing nucleus (red). After one hour incubation with a compound, the cells were quenched with fixative (formaldehyde) and the plate was read on Cellomics ArrayScan HCS Reader using the GPCR Bioapplication. Negative results are a more uniform distribution of GFP throughout the cytoplasm and positive results are a peri-nuclear localization.
Recommended attribution: "We used the SBS Roche Transfluor image set provided by Ilya Ravkin and available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
Analysis of the data set can be downloaded from http://www.broadinstitute.org/bbbc/sbs_roche_transfluor.html
DOI: 10.6075/j08p5zqq
title: CIL:1456, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
description: Rabbit psoas skeletal muscle fibers were held at constant length and rigor induced by immersion in glycerol. The fibers were quick-frozen by contact with a liquid helium- cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 24 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

Images were recorded on Kodak 4489 film at 68,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.
DOI: 10.6075/j00k27qc
title: CIL:11847, Haemanthus katharinae, endosperm. In Cell Image Library

description: Dividing cells from the liquid endosperm of the lily Haemanthus katherinae were fixed with paraformaldehye, embedded in epoxy, and 0.5 micrometer sections prepared. Images were obtained with the Wisconsin high voltage TEM at 1MEV. For this micrograph of interphase, the grid was tilted to 55 degrees. A similar micrograph tilted to 45 degrees is grouped with this image, making a stereo pair that provides an oblique 3D view.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: elastic scattering of electrons
Visualization methods: uranyl salt
Processing history: unprocessed raw data
DOI: 10.6075/j0736qw8
title: CIL:35629, Saccharomyces cerevisiae. In Cell Image 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.
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; differences in amount of elastic light scattering
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 Cln2. Cln2 is a G1 cyclin involved in regulation of the cell cycle; activates Cdc28p kinase to promote the G1 to S phase transition; late G1 specific expression depends on transcription factor complexes, MBF (Swi6p-Mbp1p) and SBF (Swi6p-Swi4p).These phase,gfp images are part of an image group that ranges from CIL:35620-35639. 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/j0gb22zc
title: CIL:24971, Drosophila melanogaster, fat body cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; acetic acid treatment
Relation to intact cell: squashed preparation
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
description: Fat body cells from 3rd instar larvae of Drosophila melanogaster were dissected, fixed with formalin-acetic acid containing 0.1% Triton-X 100, and squashed on a glass slide. After freezing in liquid nitrogen, the cover slips removed, and the slide thawed and stained with 1% uranyl acetate, rinsed in 50% ethanol, dehydrated and transferred to amyl acetate, and covered with 2% parlodion in amyl acetate. Selected areas of the parlodion film were transferred to formvar coated EM grids, and the parlodion removed by immersion in amyl acetate (see Ris H, 1981 Stereoscopic Electron Microscopy of Chromosomes, Meth Cell Biol 22:77-96). Grids were observed using the Madison High Voltage Electron Microscope at 1 MeV.
description: High Voltage TEM image showing the series of bands and interbands characteristic of a polytene chromosome. This image of a whole mount preparation of a fat body cell polytene chromosome from Drosophila melanogaster was taken with a tilt angle of 45 degrees. The accompanying grouped image, taken at 55 degrees forms a stereo pair, providing an oblique 3D view of the chromosome.
DOI: 10.6075/j06h4gb8
title: CIL:25708, Homo sapiens, retinal pigment epithelium. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
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: Time lapse series of cell growth and division in cultured hTERT-RPE1 cells (telomerase immortalized human retinal pigment epithelium) using differential interference contrast optics. This time series is grouped in the Cell Image Library with a corresponding movie.
description: Cells were cultured on glass coverslips in 10% FBS, DMEM/F12 medium plus glutamine, HEPES, penicillin and streptomycin and examined with a Leica DMIRE2 microscope with Leica HCX PLAN APO 100x NA 1.35 DIC objective lens. images were captured at 5 second intervals with a Hamamatsu ORCA-ER2 CCD camera using Simple PCI 6.6.0.0 software.
DOI: 10.6075/j02v2fnb
title: CIL: 52365, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: Tile x=4, y=2, z=4 from BL024199_Myc_Terc
description: One z layer of a z-stack at the given tile position
DOI: 10.6075/j0r49pmd
title: CIL:40969, Floscularia ringens. 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: Differential interference contrast image of a rotifer (Floscularia ringens) feeding. Its rapidly beating cilia (hair-like structures) bring water that contains food to the rotifer. When their cilia beat, the "wheel animacules" first described by Leeuwenhoek (ca.1702) look like two wheels spinning on top. They live in reddish-brown tubes made of 
 spherical "bricks." This image won First Prize, 2011 Olympus BioScapes Digital Imaging Competition©.
DOI: 10.6075/j01z43vc
title: CIL: 51749, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

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

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
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
DOI: 10.6075/j0xs5vft
title: CIL:35764, 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
Processing history: unprocessed raw data
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Clb2. Clb 2 is a cyclin-dependent protein kinase regulator, involving in G2/M transition of mitotic cell cycle and positively regulating spindle pole body separation. These phase and GFP images are part of an image group containing CIL 35760-35779. Note that there are additional groups of images of other cell cycle regulator proteins by the same authors available 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 read the microscopy section of the referenced paper for details before image analysis.
DOI: 10.6075/j0n58k4x
title: CIL:11968, uncultured Pyrsonympha sp.. In Cell Image Library

description: See: G.M. Langford and S. Inoue 1979. Motility of the microtubular axostyle in Pyrsonympha. J. Cell Biol 80:521-538.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: polarization microscopy
Parameter imaged: retardance
Source of contrast: form birefringence
Visualization methods: visualization of contiguous regions
Data qualification: Processed
description: The movie shows the rhythmic movement of the termite flagellate Pyrsonympha, a symbiont that lives in the hindgut. The motile structure is a complex of ~2,000 aligned microtubules, the axostyle which is highly birefringent and hence readily seen with polarizing microscopy. The movement is thought to be brought about by an ordered wave-like sliding between adjacent microtubules.
DOI: 10.6075/j0sb44p5
title: CIL:31932, Homo sapiens, retinal pigment epithelium. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
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: Movie of cell growth and division in cultured hTERT-RPE1 cells (telomerase immortalized human retinal pigment epithelium) using DIC optics. This movie and the stack of time series images used to prepare them are grouped in the Cell Image Library.
description: Cells were cultured on glass coverslips in 10% FBS, DMEM/F12 medium plus glutamine, HEPES, penicillin and streptomycin and examined with a Leica DMIRE2 microscope with Leica 100x HCX PLAN APO NA 1.35 DIC objective lens. images were captured at 30 sec intervals with a Hamamatsu ORCA-ER2 CCD camera using Simple PCI 6.6.0.0 software.
DOI: 10.6075/j00863vx
title: CIL:48759, Mus musculus, MC38-Cerulean cancer cells. In Cell Image Library

description: Item type: confocal microscopy
description: Mice were euthanized and tumors were freshly explanted. 1-2 mm thick sections were cut at different depths and kept in PBS during the imaging session. Fluorescent confocal microscopy was done using a Leica SP5 II TCS tandem scanner 2-photon spectral confocal microscope with XY motorized stage, using a 25X/NA 0.95 water lens from Leica.
description: To determine the origin (local vs. circulating) of tumor associated fibroblasts, a parabiotic pair of mice was created where only one mouse expressed EGFP under the control of the type I collagen alpha-1 promoter (COL-EGFP), and the other mouse expressed DsRed ubiquitously. On each mouse of the parabiotic pair, MC38-Cerulean cancer cells were injected on the distal flank. This folder contains images from the tumor grown in the COL-EGFP mouse, freshly explanted and analyzed ex vivo. The blue channel shows cancer cells, the red channel shows DsRed cells, the green channel shows COL-EGFP+ fibroblasts.
 
Image name: 110613 COLEGFP tumor side 63x means 25x water.lif - 3
 
Project: 20389
DOI: 10.6075/j0kw5fhp
title: CIL: 51737, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
description: A novel cell population analysis to quantify both initial and long-term drug effects, namely pseudopod adaptation and recovery following an initial drug-induced perturbation, adding drug slowly in 1/4 increments over 90 minutes.
description: Imaging mode: DICM
Visualization methods: Spinning disc confocal DICM & widefield DICM Using a Nikon TiE microscope equipped with a 40x, 0.95 N.A. objective and a Hamamatsu ORCA-Flash 4.0 V3 Digital CMOS camera, or a Nikon TiE spinning-disc confocal microscope equipped with a Yokogawa CSU-X1 scanning unit, an Andor iXon 888 EMCCD camera, and a 60x, 1.3 N.A. water-immersion objective or a 40x, 0.95 N.A. objective
DOI: 10.6075/j00z71vc
title: CIL:47385, Staphylococcus aureus, neutrophil, endothelial cell. In Cell Image Library

description: Visualization of neutrophil recruitment in capillaries proximal to agarose beads. (Figure 5 - Venular data)
description: Mice were anesthetized with ketamine/xylazine, and then subcutaneous tissue on a dorsal flap was exteriorized. GFP staphylococcus aureus beads were inserted. Antibodies were injected into the vasculature to label neutrophils (red) and endothelial cells (blue). Blocking antibodies against the molecule Mac1 were administered after 2 hours of infection.
description: Relation to intact cell: intact cells-in vivo imaging
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Source of contrast: antibody labelling
Processing history: Converted from volocity to .avi
DOI: 10.6075/j00r9p0q
title: CIL: 52796, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given tile position
description: Tile x=1, y=1, 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
DOI: 10.15468/dl.wheubn
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hypsolebias marginatus",
 "DecimalLatitude is not null",
 "DecimalLongitude is not null"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014747-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x3scph
title: Occurrence Download

description: A dataset containing 84 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation, Occurrence evidence, Observation)",
 "Geometry POLYGON((2.85626 48.82103,3.00184 48.82103,3.00184 48.95066,2.85626 48.95066,2.85626 48.82103))",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "PublishingOrg is 1928bdf0-f5d2-11dc-8c12-b8a03c50a862",
 "TaxonKey is Pipistrellus pipistrellus",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 84 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014749-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8r27px
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.29_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cypripedium flavum"
 ]
}

 The dataset includes 9 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014750-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.