cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0vt1s3q
title: CIL:34562, Drosophila melanogaster, muscle cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide; uranyl salt; lead salt
Processing history: digitized film
Data qualification: Processed;spatialmeasurements
description: Tissue was dissected using a freeze-fracture technique, fixed in 2.5% glutaraldehyde in 0.1 M sodium cacadylate buffer, pH 7.4, post-fixed in 2% osmium tetroxide solution, stained in 1% uranyl acetate, and embeddeded in EMbed 812 resin. Sections were post-stained with 2% uranyl acetate and stained with Reynolds's Lead Citrate. Images were obtained using transmission electron microscopy techniques, employing a Phillips CM-100 transmission electron microscope. Images were taken on Kodak EM 4489 film, scanned with a Microtek ScanMaker i900, and post-processed using Adobe Photoshop CS4. This image was taken at a magnification of 8900x.
description: Drosophila melanogaster thoracic tergotrochanter muscle from a four week-old wild-type animal. A longitudinal section of myocyte is displayed. Sections of parallel myofibrils are seen with distinguishable sarcoplasmic reticulum.
DOI: 10.6075/j0610z8t
title: CIL:34538, Homo sapiens, retinal pigment epithelium. In Cell Image Library

description: Movie showing motility and morphology of cultured hTERT-RPE1 cells (telomerase immortalized human retinal pigment epithelium) arrested in G1 using 0.08 uM nocodazole (Uetake and Sluder 2010, Curr Biol 20:1666-1671).
The time series used to create the movie is gropued in the Cell Image Library.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: phase contrast microscopy
Parameter imaged: elastic scattering of photons
Source of contrast: differences in amount of elastic light scattering
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
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 10x NA 0.3 phase contrast objective lens. Images were captured at 3 minute intervals with a Hamamatsu ORCA-ER2 CCD camera using HC Image 2.0.1.11 software.
DOI: 10.6075/j0qf8rjr
title: CIL:34523, Neisseria gonorrhoeae, motile cell, bacteria. In Cell Image Library

description: The video is a representative movie of baceria incubated in DMEM and polylysine for 3 h on top of an array of pilars of stiffness 500 pN/micron. The video is real time and shows the behavior of one or two bacteria for 23 s after 3 h of incubation. The video relates to CIL: 34521 and 34522, which show bacteria incubated in different media. The pilars are 3 micron apart center to center. The video is DIC microscopy with the focus on the top of the pilars. See the absence of motions in this media. This video corresponds to Video 4 from PLoS Biol. 2008 Apr 15;6(4):e87.
description: Preparation: whole mounted tissue
Relation to intact cell: living tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy; force 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: A pulling force exerted on a pillar, such as that imposed by an attached pilus fiber, causes a displacement of the pillar tip. The displacement can be correlated to the force applied on the pillar after proper calibrations. All optical microscope images were obtained on conventional inverted microscopes (either Olympus IX 71 or Zeiss Axiovert 100).
DOI: 10.6075/j0m61k9j
title: CIL:34563, Drosophila melanogaster, flight muscle cell. In Cell Image Library

description: Drosophila melanogaster thoracic indirect flight muscle from a four week-old wild-type animal. Here, an oblique section of myocyte is displayed. Sections of parallel myofibrils are visible between densely packed mitochondria.
description: Preparation: glutaraldehyde fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide; uranyl salt; lead salt
Processing history: digitized film
Data qualification: Processed;spatialmeasurements
description: Tissue was dissected using a freeze-fracture technique, fixed in 2.5% glutaraldehyde in 0.1 M sodium cacadylate buffer, pH 7.4, post-fixed in 2% osmium tetroxide solution, stained in 1% uranyl acetate, and embeddeded in EMbed 812 resin. Sections were post-stained with 2% uranyl acetate and stained with Reynolds's Lead Citrate. Images were obtained using transmission electron microscopy techniques, employing a Phillips CM-100 transmission electron microscope. Images were taken on Kodak EM 4489 film, scanned with a Microtek ScanMaker i900, and post-processed using Adobe Photoshop CS4. This image was taken at a magnification of 11500x.
DOI: 10.6075/j0vm4c9h
title: CIL:34561, Drosophila melanogaster, flight muscle cell. In Cell Image Library

description: Drosophila melanogaster thoracic indirect flight muscle from a four week-old wild-type animal. A longitudinal section of myocyte is displayed. Sections of parallel myofibrils are visible between densely packed mitochondria.
description: Preparation: glutaraldehyde fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide; uranyl salt; lead salt
Processing history: digitized film
Data qualification: Processed;spatialmeasurements
description: Tissue was dissected using a freeze-fracture technique, fixed in 2.5% glutaraldehyde in 0.1 M sodium cacadylate buffer, pH 7.4, post-fixed in 2% osmium tetroxide solution, stained in 1% uranyl acetate, and embeddeded in EMbed 812 resin. Sections were post-stained with 2% uranyl acetate and stained with Reynolds's Lead Citrate. Images were obtained using transmission electron microscopy techniques, employing a Phillips CM-100 transmission electron microscope. Images were taken on Kodak EM 4489 film, scanned with a Microtek ScanMaker i900, and post-processed using Adobe Photoshop CS4. This image was taken at a magnification of 11500x.
DOI: 10.6075/j0r49pc8
title: CIL:34522, Neisseria gonorrhoeae, motile cell, bacteria. In Cell Image Library

description: Preparation: whole mounted tissue
Relation to intact cell: living tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy; force 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 video is a representative movie of bacteria incubated in DMEM with BSA for 3 h on top of an array of pilars of stiffness 500 pN/micron. The video is real time and shows the behavior of one or two bacteria for 23 s after 3 h of incubation. The video relates to CIL: 34521 and 34523, which show bacteria incubated in different media. The pilars are 3 micron apart center to center. The video is DIC microscopy with the focus on the top of the pilars. See the transient pulls and the fact that the two bacteria are not as tightly connected to the pillars in this media. This video corresponds to Video 3 from PLoS Biol. 2008 Apr 15;6(4):e87.
description: A pulling force exerted on a pillar, such as that imposed by an attached pilus fiber, causes a displacement of the pillar tip. The displacement can be correlated to the force applied on the pillar after proper calibrations. All optical microscope images were obtained on conventional inverted microscopes (either Olympus IX 71 or Zeiss Axiovert 100).
DOI: 10.6075/j0h130pj
title: CIL:34520, Neisseria gonorrhoeae, motile cell, bacteria. In Cell Image Library

description: This video shows a typical N. gonorrhoeae microcolony interacting with the tips of our micropillar force sensing device. The video is speeded 10 times (×10) and the pilars are 3 micron apart center to center. A pulling force exerted on a pillar, such as that imposed by an attached pilus fiber, causes a displacement of the pillar tip. The displacement can be correlated to the force applied on the pillar after proper calibrations. Video corresponds to Video 1 from PLoS Biol. 2008 Apr 15;6(4):e87.
description: All optical microscope images were obtained on conventional inverted microscopes (either Olympus IX 71 or Zeiss Axiovert 100).
description: Preparation: whole mounted tissue
Relation to intact cell: living tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy; force 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/j0qc02fd
title: CIL:34536, Tetrahymena pyriformis, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: 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; unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: High resolution view of the nuclear envelope of both the macronucleus, seen here, and the micronucleus consists of 2 membranes containing numerous perforations called pores. Proteins are imported through these pores and ribosomal subunits are transported out of the macronucleus through the same pores. TEM taken on 8/16/67 by R. Allen with a Philips 200 operating at 60kV. Neg. 12,400X. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis.
DOI: 10.6075/j00r9ppp
title: CIL:56023, Homo sapiens. In Cell Image Library

description: Scans of H&E-stained histology slides of biopsied tissue from endoscopy. Captured with MikroScan SL5 in SVS TIFF format with .tif file extension.
description: Scan 07_A_DD_C -- The dataset consists of 951 tissue section scans taken from 167 H&E-stained whole slides from 18 pediatric inflammatory bowel disease (IBD) patients. Slide section scans are provided as-is without any initial image pre-processing, normalization, or cropping. Labels are provided at the patient, slide (anatomic site), and section (tissue slice) levels. Each slide is labelled with biopsy site and normal or abnormal classification per the surgical pathology report. Each tissue section scan from an abnormal slide is further classified as normal or abnormal by pathologist. Files may be viewed and annotated using standard, opensource slide-viewing software, such as Aperio ImageScope, OpenSlide​​, TiffSlide, and QuPath​​.
description: Imaging mode: Static digital pathology tissue scans
Visualization methods: Hematoxylin and eosin
DOI: 10.6075/j0ht2n00
title: CIL:34521, Neisseria gonorrhoeae, motile cell, bacteria. In Cell Image Library

description: Preparation: whole mounted tissue
Relation to intact cell: living tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy; force 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 video is a representative movie of baceria incubated in DMEM for 3 h on top of an array of pilars of stiffness 500 pN/micron. The video is real time and shows the behavior of one or two bacteria for 23 s after 3 h of incubation. The video relates to CIL: 34522 and 34523, which show bacteria incubated in different media. The pilars are 3 micron apart center to center. The video is DIC microscopy with the focus on the top of the pilars. See the already deflected pillars around the bacterium and both transient and sustained pulls. This video corresponds to Video 2 from PLoS Biol. 2008 Apr 15;6(4):e87.
description: A pulling force exerted on a pillar, such as that imposed by an attached pilus fiber, causes a displacement of the pillar tip. The displacement can be correlated to the force applied on the pillar after proper calibrations. All optical microscope images were obtained on conventional inverted microscopes (either Olympus IX 71 or Zeiss Axiovert 100).
DOI: 10.6075/j0bp01rq
title: CIL:34517, Homo sapiens, cervical carcinoma. In Cell Image Library

description: Preparation: chemically fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain; distribution of a specific protein
Processing history: 3D-deconvolution
Data qualification: Processed
description: Immunolabeling of endogenous splicing factor SC35 (red) and transfected FP-tagged lamin B receptor. Image stack was acquired using a Deltavision deconvolution microscope.
DOI: 10.6075/j0n015tj
title: CIL:345, Mus musculus, skeletal muscle cell. In Cell Image Library

description: Thin section electron microscopy of gastrocnemius (skeletal) muscle from a wild type mouse.

Sample was viewed with a Hitachi 7600 electron microscope (accelerating voltage 80 KV) and imaged with an AMT digital camera. Image taken at 20,000X magnification.

This image is part of a set of wild type gastrocnemius muscle images that served as controls for the study of the delta-sarcoglycan knockout mouse. Both the set of wild-type and delta-sarcoglycan knockout mouse images are part of The CELL: an image library.

Reference: Nat Med. 2008 Apr;14(4):442-7. 
Genetic and pharmacologic inhibition of mitochondrial-dependent necrosis attenuates muscular dystrophy.
Millay DP, Sargent MA, Osinska H, Baines CP, Barton ER, Vuagniaux G, Sweeney HL, Robbins J, Molkentin JD (tissue preparation described in Fewell JG, et al. A treadmill exercise regimen for identifying cardiovascular phenotypes in transgenic mice. Am J Physiol. 1997;273:H1595–H1605)
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: uranyl salt; lead salt
Visualization methods: detection of electrons
Processing history: unprocessed raw data
DOI: 10.6075/j0959gvc
title: CIL:344, Mus musculus, skeletal muscle cell. In Cell Image Library

description: Thin section electron microscopy of gastrocnemius (skeletal) muscle from a wild type mouse.

Sample was viewed with a Hitachi 7600 electron microscope (accelerating voltage 80 KV) and imaged with an AMT digital camera. Image taken at 20,000X magnification.

This image is part of a set of wild type gastrocnemius muscle images that served as controls for the study of the delta-sarcoglycan knockout mouse. Both the set of wild-type and delta-sarcoglycan knockout mouse images are part of The CELL: an image library.

Reference: Nat Med. 2008 Apr;14(4):442-7. 
Genetic and pharmacologic inhibition of mitochondrial-dependent necrosis attenuates muscular dystrophy.
Millay DP, Sargent MA, Osinska H, Baines CP, Barton ER, Vuagniaux G, Sweeney HL, Robbins J, Molkentin JD (tissue preparation described in Fewell JG, et al. A treadmill exercise regimen for identifying cardiovascular phenotypes in transgenic mice. Am J Physiol. 1997;273:H1595–H1605)
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: uranyl salt; lead salt
Visualization methods: detection of electrons
Processing history: unprocessed raw data
DOI: 10.15468/dl.v63zuw
title: Occurrence Download

description: A dataset containing 14 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.continent = 'ASIA'
 AND occurrence.countrycode = 'CN'
 AND (CAST(occurrence.taxonkey AS INTEGER) = 5231190 OR CAST(occurrence.acceptedtaxonkey AS INTEGER) = 5231190 OR CAST(occurrence.kingdomkey AS INTEGER) = 5231190 OR CAST(occurrence.phylumkey AS INTEGER) = 5231190 OR CAST(occurrence.classkey AS INTEGER) = 5231190 OR CAST(occurrence.orderkey AS INTEGER) = 5231190 OR CAST(occurrence.familykey AS INTEGER) = 5231190 OR CAST(occurrence.genuskey AS INTEGER) = 5231190 OR CAST(occurrence.specieskey AS INTEGER) = 5231190)
 AND (occurrence."year" &gt;= 2012 AND occurrence."year" &lt;= 2025)
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (occurrence.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 14 records were derived from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009312-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0kh0nn8
title: CIL:56063, Homo sapiens. In Cell Image Library

description: Imaging mode: Static digital pathology tissue scans
Visualization methods: Hematoxylin and eosin
description: Scans of H&E-stained histology slides of biopsied tissue from endoscopy. Captured with MikroScan SL5 in SVS TIFF format with .tif file extension.
description: Scan 07_H_CT_A -- The dataset consists of 951 tissue section scans taken from 167 H&E-stained whole slides from 18 pediatric inflammatory bowel disease (IBD) patients. Slide section scans are provided as-is without any initial image pre-processing, normalization, or cropping. Labels are provided at the patient, slide (anatomic site), and section (tissue slice) levels. Each slide is labelled with biopsy site and normal or abnormal classification per the surgical pathology report. Each tissue section scan from an abnormal slide is further classified as normal or abnormal by pathologist. Files may be viewed and annotated using standard, opensource slide-viewing software, such as Aperio ImageScope, OpenSlide​​, TiffSlide, and QuPath​​.
DOI: 10.6075/j0bz65k5
title: CIL: 52417, 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=5, y=2, z=14 from BL024199_Myc_Terc
description: One z layer of a z-stack at the given tile position
DOI: 10.6075/j01g0kvt
title: CIL: 52849, 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=4, z=5 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: 10.6075/j04x57cq
title: CIL: 52913, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Image 11, z=6 from SC_007
description: One z layer of a z-stack at the given image
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