cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0n58knn
title: CIL:2185, 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: 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 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.
DOI: 10.57967/hf/6847
title: HW5K
DOI: 10.15468/dl.9kzry3
title: Occurrence Download

description: A dataset containing 3296 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Juglans mandshurica",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Human Observation)",
 "OccurrenceStatus is Present",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than or equal to 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 },
 "EventDate is greater than or equal to 1991-01-01",
 "EventDate is less than or equal to 2025-10-31"
 ]
}

 The dataset includes 3296 records from 105 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009274-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0mp52td
title: CIL: 52386, 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=4, y=5, z=4 from BL024199_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/j07m06xd
title: CIL:7352, notopthalmus viridescens, erythrocyte. In Cell Image Library

description: Newt (Notopthalmus viridescens erythrocytes were isolated in 0.1M KCl, spread on the surface of Na-citrate, picked up on formvar-carbon films, fixed with glutaraldehyde and negatively stained with 2% uranyl acetate. Images were recorded at 40KX and accelerating voltage of 1MeV at the University of Wisconsin HVEM facility.This image was taken with a specimen tilt of 45 degrees. A grouped image of the same field at a 55 degree tilt provides an oblique stereo view of the tangle of chromatin fibers in the dispersed nucleus.
description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: spread nucleus
Item type: film
Imaging mode: transmission electron microscopy (TEM); illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: negative staining; uranyl salt
Processing history: unprocessed raw data
DOI: 10.6075/j0cz36j9
title: CIL: 50697, 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: Serial electron microscopy; focused ion beam scanning electron mictoscopy (FIB-SEM)
Visualization methods: Heavy metal stain (osmium tetroxide, potassium ferrocyanide, tannic acid), immunogold labeling using 10 nm gold beads
description: "Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample. 
3.1_Cell_3_Raw_Image_Stack is a multipage TIFF file consisting of 208 individual EM sections acquired at 15 nm milling step, resulting in 2.6×2.6×15 nm³ voxel size. Note: some stereocilia are missing their tips and although segmented, were excluded from the MATLAB analysis.
This file is a part of Dataset 3, comprised of files related to the Cell #3 of current study. The numbering order of the files reflects the order of operations performed during the analysis."
DOI: 10.6075/j0028q36
title: CIL:47513, Staphylococcus aureus, neutrophil, endothelial cell. In Cell Image Library

description: Visualization of neutrophil recruitment in capillaries proximal to S. aureus beads. (Figure 3 - A4 block)
description: Mice were anesthetized with ketamine/xylazine, and then subcutaneous tissue on a dorsal flap was exteriorized. GFP labelled S. aureus beads were inserted. Antibodies were injected into the vasculature to label neutrophils (red) and endothelial cells (blue)
description: Relation to intact cell: intact cells-in vivo imaging
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Processing history: Converted from volocity to .avi
DOI: 10.6075/j0k07312
title: CIL:26543, Mus musculus, fibroblast. In Cell Image Library

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 (Scr) for 2 days, treated with DMSO for 30 min., and stained for βPIX (green) and vinculin (red). In scrambled siRNA-treated cells treated with DMSO, vinculin localized to large focal adhesions at the cell periphery that overlapped with βPIX. βPIX siRNA had little effect on its own. 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. 6A, “Requirement for βPIX in MII-regulated cell protrusion and adhesion.” J. Cell Biol. 2010. Vol. 190(4):663–674.
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. siRNA transfected NIH3T3 cells were treated with DMSO for 30 min, and co-stained for betaPIX (green) and vinculin (red). Images were captured by Olympus IX81-ZDC inverted microscope with UPlanFL N 40X objective.
DOI: 10.6075/j0rr1x3r
title: CIL:39027, Danio rerio, neuron. In Cell Image Library

description: Confocal micrograph of the head region of a transgenic zebrafish embryo. The large circular structure is the eye, showing the structure of the retina. Some neurons in the brain are highlighted in green by GFP expressed under the control of a specific promoter Dlx4/6. The DLX proteins are postulated to play a role in forebrain and facial development. Therefore, the GFP is only 'switched on' in developing neurons that require this gene. The microtubules in neuronal processes have been labelled using an antibody for tubulin (red).
description: Preparation: chemically fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label; distribution of epitope
Visualization methods: EGFP; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
description: Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
DOI: 10.6075/j0xs5tb2
title: CIL:35846, Saccharomyces cerevisiae. In Cell Image Library

description: The images were acquired using a 60x 1.42 NA objective lens on Delta Vision system equipped with CoolSNAP_HQ2 / HQ2-ICX285. Please read the microscopy section of the referenced paper for details before image analysis.
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Cdc15, a protein kinase involves in cytokinesis. These phase and GFPimages are part of an image group containing CIL 35840-35859. Note that there are additional groups of images of other cell cycle regulator proteins by the same authors available in the Library.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission; elastic scattering of photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0sn08dt
title: CIL: 51165, 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: 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: ~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.
DOI: 10.6075/j0222sx4
title: CIL:9837, Nassula, 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 from negative scanned for Photoshop
Data qualification: Processed;spatialmeasurements
description: Cytopharyngeal rods, composed of microtubular bundles, form the wall of the basket. Rod lamellae are attached to one side of each rod. TEM taken on 3/13/69 by R. Allen with Philips 300 operating at 60kV. Neg. 16,000X. Bar = 0.5µm. A print of the negative was scanned and processed in Photoshop. This image is best used for qualitative analysis. A high resolution image (CIL:7664) is 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.

Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j05b0170
title: CIL:12298, Taricha granulosa, epithelial cell of lung. In Cell Image Library

description: The retrograde flow of microtubules oriented perpendicular to the leading edge inthe lamellipodium is not coupled to the movement of immediately adjacent lammellipodium. Primary cultures of newt (Taricha granulosa) lung epithelial cells were microinjected with 
X-rhodamine actin and Cy2 tubulin in coinjection. Dual-wavelength time-lapse FSM was performed on a spinning disk confocal microscope system. Light from a 50-mW Krypton-Argon ion laser (Melles Griot, OmniChrome) was delivered by a single-mode fiber optic (Point Source) to a Yokogawa spinning disk confocal scan-head (Ultra-View; PerkinElmer) on an inverted microscope (TE300 Quantum; Nikon). Excitation wavelength was selected by a filter-wheel apparatus (Sutter Instruments Co.) containing excitation filters for 488 and 568 nm (Chroma) and an opaque disk used as an excitation shutter. Emission was selected by multiple bandpass dichromatic mirror and emission filter (Chroma). Images were collected by a 100x 1.4NA Plan-Apo DIC objective lens (Nikon) and captured with an Orca 2 camera (Hamamatsu). Microscope functions were controlled by MetaMorph software (Universal Imaging). One set of sequential images of the specimen using 488 nm light for Cy2 tubulin and 568 nm light for X-rhodamine f-actin was collected in the ventral focal plane at 10s intervals. Images were processed as follows: (1) background subtraction; (2) 3 x3 low pass filter; (3) unsharp mask filter; (4) color coding MT images green and f-actin images red; and (5) color combining into 24-bit RGB images. Video corresponds to Fig.3B and video 5 in J Cell Biol, 158:31-37, 2002
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: spinning disk confocal microscopy; fluorescent speckle microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: X-Rhodamine; Cy2
Processing history: background subtraction, 3X3 low pass filter, unsharp mask
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0862g10
title: CIL: 53001, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: One z layer of a z-stack at the given image
description: Image 1, z=10 from SC_028
DOI: 10.6075/j0s46rzw
title: CIL:32065, Homo sapiens, osteocarcenoma. In Cell Image Library

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
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
DOI: 10.6075/j0610zm9
title: CIL:1612, Caenorhabditis elegans. In Cell Image Library

description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 0 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: 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
DOI: 10.6075/j0x066b2
title: CIL:1608, 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: 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.
DOI: 10.6075/j0jd4w2q
title: CIL:1607, Caenorhabditis elegans. In Cell Image Library

description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 0 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
DOI: 10.6075/j0n29w40
title: CIL:13195, 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 1.0 micrometer sections prepared. Images were obtained with the Wisconsin high voltage TEM at 1MEV. For this low magnification survey micrograph of chromosomes at prophase, the grid was tilted to 60 degrees. A similar micrograph tilted to 40 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/j0k936qv
title: CIL:9911, Opercularia [NCBITaxon:168247], Opercularia coarctata, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: An image of the contractile vacuole and the spongiome decorated tubules showing V-type proton pumps extending from the cytosolic side of the tubules; also detail of the micronucleus. TEM taken on 6/10/69 by R. Allen with Philips 300 operating at 60kV. Neg. 14,800X. Bar = 0.25µm. A print of the negative was scanned and processed in Photoshop. This image is best used for qualitative analysis. A high resolution image (CIL:7305) is 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/).
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 from negative scanned for Photoshop
Data qualification: Processed;spatialmeasurements