cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j01j98x3
title: CIL:16244, Mus musculus, pyramidal cell, hippocampal granule cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label; distribution of a specific protein
Visualization methods: 4',6-diamidino-2-phenylindole (DAPI); EGFP; Alexa Fluor 488; Alexa Fluor 568
Data qualification: Raw
description: Distribution of hippocampal neurons expressing EGFP from the Nr4a1/Nur77 promoter (Tg(Nr4a1-EGFP)GY139Gsat, www.gensat.org) in hippocampal CA1 colabelled for the vesicular glutamate transporter (VGluT1, red, Invitrogen polyclonal, 1:1000) and stained with DAPI (blue) to show cell layers. EGFP expression was amplified with chicken anti-GFP (Abcam, 1:2000). VGluT1 labels excitatory terminals synapsing in the molecular layer of the dentate gyrus, mossy fiber terminals in CA3 and dendritic fields of the pyramidal cells in stratum orien and stratum radiatum. Nr4a1-EGFP is heavily expressed by CA1 pyramidal cells and to a lesser extent in CA3 pyramidal cells with sparse cells in the dentate gyrus (see associated images). Section (40 um, sagittal) was mounted with Fluoromount G and imaged with a 5X, 0.15 NA objective on a Zeiss Axiovert microscope. AF568 was excited at 562/40 nm and emission collected at 624/40 nm with Semrock filters and a single band dichroic (530-585 nm reflected, 601-800 nm transmitted). AF488 was excited at 482/35 nm and emission collected at 536/40 nm with Semrock filters and a single band dichroic (446-499 nm reflected, 513-735 nm transmitted). DAPI was excited at 350/50 nm and emission collected at 460/50 nm with a CLP400 dichroic (Chroma). Single images were captured for each channel using a Zeiss Axiocam MR CCD and pseudo-colored using Axiovision. Linear background subtraction was used on the presented image. See Davis and Puhl (2011), Pubmed ID 21305052, for a detailed staining protocol and images of EGFP expression in the striatum and amygdala in this strain. This image is part of a series characterizing EGFP expression from the Nr4a1 promoter throughout the brain.
DOI: 10.6075/j03r0rrx
title: CIL:39062, Mus musculus, male germ cell, Sertoli cell. In Cell Image Library

description: Preparation: chemically fixed tissue
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: modes of light microscopy
Parameter imaged: absorption of illumination
Source of contrast: differences in adsorption or binding of stain
Visualization methods: toluidine blue
Processing history: unprocessed raw data
description: B0007567 Male germ cells. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
description: This light micrograph shows the outside edge of two seminiferous tubules of a mouse testis. This section is a 1um thick transverse section, stained with toluidine blue to highlight the cells, with the nucleus staining a darker blue. The dark blue line separating the two seminiferous tubules consists mostly of myoid (muscle) tissue. The majority of cells seen in this image (arranged in layers) are germ cells, which, by repeated cell division, eventually produce spermatozoa. Chromosomes are visible in most of the nuclei of the cells. The cell with a deeply-stained nucleus and even darker nucleolus is a Sertoli cell ('nurse cell') that has fine cytoplasmic extensions branching between the other cells to nurture the developing germ cells.
DOI: 10.6075/j0jm2977
title: CIL: 52994, 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=3 from SC_028
DOI: 10.6075/j0bk19z2
title: CIL:50352, Mus musculus, Spinal cord neuron. In Cell Image Library

description: Biological samples are frequently stained with heavy metals in preparation for examining the macro, micro and ultra-structure using X-ray microtomography and electron microscopy. A single X-ray microtomography scan reveals detailed 3D structure based on staining density, yet it lacks both material composition and functional information. Using a commercially available polychromatic X-ray source, energy integrating detectors and a two-scan configuration labelled by their energy- High and Low, we demonstrate how a specific element, here shown with iron, can be detected from a mixture with other heavy metals. With proper selection of scan configuration, achieving strong overlap of source characteristic emission lines and iron K-edge absorption, iron absorption was enhanced enabling K-edge imaging. Specifically, iron images were obtained by scatter plot material analysis, after selecting specific regions within scatter plots generated from the High and Low scans. Using this method, we identified iron rich regions associated with an iron staining reaction that marks the nodes of Ranvier along nerve axons within mouse spinal roots, also stained with osmium metal commonly used for electron microscopy.

30kVp with no filtration .
description: Item type: recorded image
Imaging mode: X-ray micrograph
Source of contrast: Fe and Os staining
description: XRM was performed on a Versa 510, (Carl Zeiss X-ray Microscopy, Pleasanton, CA 94588). The Versa 510 is equipped with a polychromatic tungsten source, tunable in the voltage range 30-160kVp. Scan configuration: "Low" -30kVp peak tube potential without filtration, exposure time 20-90sec. "High"-60kVp peak tube potential, filtration 25μm thick iron filter, exposure time 10-120sec. Common scan conditions: binning 1, source-rotation axis distance 7.5mm, detector-rotation axis distance 5mm, pixel size 0.394μm, optical magnification x20, rotation angle -180° to +180°, number of views 3201. Iron filtration used a 0.001"x1"x2" foil placed at the X-ray tube exit slit. The foil was of 3N5 purity and sold by ESPI Metals, Ashland, OR 97520.
DOI: 10.6075/j09g5m29
title: CIL:1945, 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/j0qz28k9
title: CIL:38857, Arabidopsis thaliana, leaf. In Cell Image Library

description: Leaves from the arc5 plastid division mutant of Arabidopsis thaliana were fixed, embedded, sectioned, reacted with antibodies to the FtsZ1-1 protein, a prokaryotic cell division protein that is a structural homolog of tubulin. The protein is localized at the site of division which occurs by constricting at the chloroplast mid-point. The upper panel shows the fluorescence image, the lower panel, the corresponding DIC image.
description: Preparation: formaldehyde fixed tissue; tissue in wax embedment
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: fluorescence microscopy; differential interference contrast microscopy
Parameter imaged: fluorescence emission; optical path length gradient
Source of contrast: distribution of epitope; boundaries between regions with different refractive index
Visualization methods: Fluorescein (FITC)
Data qualification: Processed
description: Leaves were fixed in FAA (formalin acetic acid), embedded in low melting point polyester wax, and 7 micrometer sections cut and attached to poly-L-lysine slides. Sections were de-waxed, treated with an antigen retrieval procedure, and processed for immunofluorescence using incubation with an affinity purified polyclonal antibody, followed by FITC-conjugated secondary antibody. Slides were viewed with an Olympus BH2 microscope equipped with DIC optics. Images were recorded on film, or a video camera (Optronics DEI 750 using a 100x 1.25 NA objective lens. See S. Vitha et al. 2001 J Cell Biol 153:111-119.
DOI: 10.6075/j0rf5sm7
title: CIL:48825, Mus musculus, MC57-Cerulean. In Cell Image Library

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, MC57-Cerulean cancer cells were injected on the distal flank. This folder contains images from the tumor grown in the DsRed 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 (absent in the DsRed mouse tumor). Image name: 120513 parab dsred tumor flank.lif - 3 

Project: 20389
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: Item type: confocal microscopy
DOI: 10.6075/j01j98nh
title: CIL:32136, Drosophila melanogaster, epithelial cell. In Cell Image Library

description: Images were acquired using a motorized Zeiss Axioplan 2 and a Axiocam MRm camera, and are provided courtesy of the laboratory of David Sabatini at the Whitehead Institute for Biomedical Research. Each image is roughly 512 x 512 pixels, with cells roughly 25 pixels in diameter, and 80 cells per image on average. 

Algorithms for finding boundaries between adjacent cells may use the union of the manually outlined cells as input. They may also use the manually outlined nuclei as seed regions. This ensures that the algorithms are compared according to their ability to find boundaries betwen adjacent cells, and not the orthogonal problems of segmenting nuclei and distinguishing foreground (cells) from background.

To compare an algorithm's results to the manual outlines, define the relevant boundary pixels as the pixels that are on the boundary found by the algorith and that are not adjacent to any background pixels. For each relevant pixel, compute the Euclidean distance to the corresponding pixel on the manually found outline. Report the percentage of relevant pixels that are within two pixels of the corresponding pixel on the manually found outline.
description: Drosophila melanogaster Kc167 cells were stained for DNA (to label nuclei, red) and actin (a cytoskeletal protein, to show the cell body, green). Each image is a dual channel fluorescent image followed by a line tracing of the nuclei and a line tracing of the cell boundary. These images are provided as a tool for testing algorithims to find nuclei and the boundaries between adjacent cells.

Chris Gang outlined the nuclei and cells.
Please use the following recommended citation when using this data. "We used the Drosophila Kc167 2 image set (Jones et al., Proc. ICCV Workshop on Computer Vision for Biomedical Image Applications, 2005), 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; hand drawn contour
Imaging mode: fluorescence microscopy
Parameter imaged: distribution of a specific protein; distribution of DNA
Source of contrast: distribution of a specific protein
Processing history: unprocessed raw data; tracing
Data qualification: Raw
DOI: 10.6075/j0w66k2s
title: CIL:826, Notophthalmus viridescens, oocyte. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: microscopy
Imaging mode: transmission electron microscopy (TEM); detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: electron-dense stain; visualization of contiguous regions; negative staining; uranyl salt
Processing history: unprocessed raw data
description: Amphibian oocytes have many copies of rRNA genes that are actively transcribed. Newt oocyte nuclei were dissected, allowed to swell in a low ionic strength high pH buffer, centrifuged through a sucrose-formaldehyde cushion onto EM grids coated with carbon films, and, in this iamge, stained with aqueous uranly acetate. The strand shows a single rRNA transcript starting at top left and terminating toward the lower right. The tree-like transcribed gene shows closely packed RNA polymerases with inceasingly large nascent rRNA transcripts as they approach the termination point. Nascent transcripts are more compact with negative than positive staining. Nucleosomes are visible in the spacer region at lower right.
DOI: 10.15468/dl.v2wruv
title: Occurrence Download

description: A dataset containing 3151 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Betula platyphylla",
 "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 3151 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009272-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j08w3cdz
title: CIL:21757, Drosophila melanogaster, epithelial. In Cell Image Library

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
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 48 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)."
DOI: 10.6075/j0nc60gp
title: CIL:2261, 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 6 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: 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/j0s75dxz
title: CIL:47554, Staphylococcus aureus, neutrophil, endothelial cell. In Cell Image Library

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
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: Visualization of neutrophil recruitment in capillaries proximal to agarose beads. (Figure 3 - Mac1)
DOI: 10.6075/j0v123n2
title: CIL:26592, Homo sapiens, cervical epithelium. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: line averaging
Data qualification: Processed
description: DRB-treated HeLa cells stably expressing BAC-encoded GFP-labeled snRNP protein U1-70K and imaged witb a PicoQuant MicroTime 200 confocal microscope using an Olympus 60x 1.2NA water immersion objective lens. DRB inhibition of transcription results in enlargement and rounding up of splicing factor compartments in which the U1-70K is enriched. From Fig 2C in Huranova et al. 2010 J Cell Biol 191:75-86.
DOI: 10.6084/m9.figshare.30496823
title: Personalized Uric Acid Monitoring via Smart Contact Lens-Trained AI for Device-Free Prediction

description: Personalized Uric Acid Monitoring via Smart Contact Lens-Trained AI for Device-Free Prediction
DOI: 10.6084/m9.figshare.30496823.v2
title: Personalized Uric Acid Monitoring via Smart Contact Lens-Trained AI for Device-Free Prediction

description: Personalized Uric Acid Monitoring via Smart Contact Lens-Trained AI for Device-Free Prediction
DOI: 10.6084/m9.figshare.30496823.v1
title: Personalized Uric Acid Monitoring via Smart Contact Lens-Trained AI for Device-Free Prediction

description: Personalized Uric Acid Monitoring via Smart Contact Lens-Trained AI for Device-Free Prediction
DOI: 10.6075/j0kh0m7g
title: CIL:26590, Homo sapiens, cervical epithelium. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: line averaging
Data qualification: Processed
description: HeLa cells stably expressing BAC-encoded GFP-labeled snRNP protein U1-70K and imaged witb a PicoQuant MicroTime 200 confocal microscope using an Olympus 60x 1.2NA water immersion objective lens. The U1-70K is confined to the nucleoplasm and enriched in splicing factor compartments and Cajal Bodies (bright dots). From Fig 2A in Huranova et al. 2010 J Cell Biol 191:75-86.
DOI: 10.6075/j0fq9vh6
title: CIL:26587, Homo sapiens, cervical epithelium. In Cell Image Library

description: HeLa cells stably expressing BAC-encoded GFP-labeled snRNP protein U1-70K-GFP and imaged witb a Leica SP5 confocal microscope using a 60x 1.4NA HCX Plan Apo objective lens. The U1-70K-GFP is confined to the nucleoplasm and enriched in splicing factor compartments and Cajal Bodies (bright dots). See Fig 1A in Huranova et al. 2010 J Cell Biol 191:75-86.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: frame averaging
Data qualification: Processed
DOI: 10.6075/j01n800b
title: CIL:26600, Homo sapiens, cervical epithelium. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP; pDsRED-Monomer-N1
Processing history: line averaging
Data qualification: Processed
description: HeLa cells stably expressing the BAC-encoded GFP-labeled hPrp8 snRNP and MS2-mRED protein and treated with doxycholine to express the E3 transgene. Shown is the mRED signal. Cells imaged witb a Leica SP5 confocal microscope using a 60x 1.4NA HCX Plan Apo objective lens. From Fig 5C in Huranova et al. 2010 J Cell Biol 191:75-86.
DOI: 10.6075/j0bz64zp
title: CIL:26591, Homo sapiens, cervical epithelium. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: line averaging
Data qualification: Processed
description: HeLa cells stably expressing BAC-encoded GFP-labeled snRNP protein U1-70K lacking the RNA-binding residues 1-197 and imaged witb a PicoQuant MicroTime 200 confocal microscope using an Olympus 60x 1.2NA water immersion objective lens. The delta-1-197U1-70K is partially accumulated in splicing factor compartments and Cajal Bodies (bright dots). From Fig 2B in Huranova et al. 2010 J Cell Biol 191:75-86.
DOI: 10.6075/j0q81bzs
title: CIL:26585, Homo sapiens, cervical epithelium. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: frame averaging
Data qualification: Processed
description: HeLa cells stably expressing BAC-encoded GFP-labeled snRNP protein hPrp8 and imaged witb a Leica SP5 confocal microscope using a 60x 1.4NA HCX Plan Apo objective lens. The hPrp8 is confined to the nucleoplasm and enriched in splicing factor compartments and Cajal Bodies (bright dots). See Fig 1A in Huranova et al. 2010 J Cell Biol 191:75-86.