cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0r211d4
title: CIL:35624, 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: 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.
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
DOI: 10.6075/j03t9g4n
title: CIL:35385, Homo sapiens, cevical carcinoma. In Cell Image Library

description: Preparation: coagulating-fixative fixed tissue; critical_point dried specimen
Relation to intact cell: whole mounted tissue
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: HeLa cells were metaphase-arrested by a 3hr treatment with colcemid, the cells mechanically broken by passage through a 22-gauge needle, exposed to hypotonic 75 mM KCl for 10 min. Samples were fixed with 3:1 methanol:acetic, treated to remove histones, spread on a water surface, picked up on formvar coated grids, critical point dried, and imaged with the Wisconsin HVEM at 1 MeV. See Ris (1978) Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:229-246; Ris (1981) Stereoscopic microscopy of chromosomes. Meth Cell Biol 22:77-96.
description: Whole human female metaphase chromosome from metaphase arrested cell swollen in hypotonic medium and treated to remove histones. The resulting residual chromosome 'scaffold' was imaged at 1 MeV. This image was taken with a specimen tilt of 55 degrees. Grouped with it is an image of the same area at 45 degrees tilt, providing an oblique stereo view of the chromosome.
DOI: 10.6075/j01c1x4w
title: CIL:55464, 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 11_G_CA_D -- 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/j0t152m1
title: CIL:35399, Drosophila melanocephala, salivary gland. In Cell Image Library

description: Preparation: chemically fixed tissue; coagulating-fixative fixed tissue
Relation to intact cell: whole mounted tissue; chromosome squash
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
description: High Voltage (1MeV) TEM image of a squash preparation of polytene chromosomes from salivary gland of 3rd instar larva of Drosophila melanogaster showing the band-interband organization. This image was captured with a specimen tilt of 46 degrees. Grouped with it is an image of the same region taken at a tilt angle of 60 degrees, providing an oblique stereo view of the structure.
description: Salivary glands were dissected, exposed to 0.07 M KCl, fixed in 3:1 acetic acid:ethanol and squashed in 50% acetic acid. Slides were frozen in liquid nitrogen, the cover slip removed, and the slide immersed in 1% uranyl acetate for 5 min followed by dehydration in ethanol and transfer to amyl acetate. 2% parlodion in amyl acetate was spread over the slide and allowed to air dry. Areas for observation were scored, released by water immersion, picked up on formvar-coated grids and observed with the Wisconsin HVEM at 1 MeV. See Ris, H 1981 Stereoscopic Electron Microscopy of chromosomes. Meth Cell Biol 22:77-96; Ris, H 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:229-246.
DOI: 10.6075/j0pk0gdp
title: CIL:56095, Homo sapiens. In Cell Image Library

description: Scan 09_B_ST_B -- 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
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.
DOI: 10.15468/dl.mb5gxm
title: Occurrence Download

description: A dataset containing 174 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Benin, Togo)",
 "TaxonKey is Detarium senegalense"
 ]
}

 The dataset includes 174 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009447-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0th8kzp
title: CIL:354, Mus musculus, skeletal muscle cell. In Cell Image Library

description: Thin section electron microscopy of gastrocnemius (skeletal) muscle from a wild type mouse. Section was stained with warm uranyl acetate stain.

Sample was viewed with a Hitachi 7600 electron microscope (accelerating voltage 80 KV) and imaged with an AMT digital camera. Image taken at 40,000X 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/j0b56hn8
title: CIL:35387, Drosophila melanocephala, salivary gland. In Cell Image Library

description: Salivary glands were dissected, fixed with paraformaldehyde, post-fixed with osmium tetroxide, and embedded in plastic. 4 micron sections were cut, stained with aqueous uranyl magnesium acetate, and observed with the Wisconsin HVEM at 1 MeV. See Ris, H 1981 Stereoscopic Electron Microscopy of chromosomes. Meth Cell Biol 22:77-96; Ris, H 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:229-246
description: Preparation: chemically fixed tissue; osmium tetroxide fixed tissue; tissue in plastic embedment; paraformaldehyde fixation
Relation to intact cell: microtome-sectioned tissue
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
description: High Voltage (1MeV) TEM image of a 'thick' section of polytene chromosome from salivary gland of 3rd instar larva of Drosophila melanogaster showing the band-interband organization. This image was captured with a specimen tilt of 56 degrees. Grouped with it is an image of the same region taken at a tilt angle of 45 degrees, providing an oblique stereo view of the structure.
DOI: 10.6075/j01j98pz
title: CIL:35389, Drosophila melanogaster, salivary gland. In Cell Image Library

description: Preparation: chemically fixed tissue; osmium tetroxide fixed tissue; tissue in plastic embedment; paraformaldehyde fixation
Relation to intact cell: microtome-sectioned tissue
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
description: High Voltage (1MeV) TEM image of a 'thick' section of polytene chromosome from salivary gland of 3rd instar larva of Drosophila melanogaster showing the band-interband organization. This image was captured with a specimen tilt of 56 degrees. Grouped with it is an image of the same region taken at a tilt angle of 45 degrees, providing an oblique stereo view of the structure.
description: Salivary glands were dissected, fixed with paraformaldehyde, post-fixed with osmium tetroxide, and embedded in plastic. 4 micron sections were cut, stained with aqueous uranyl magnesium acetate, and observed with the Wisconsin HVEM at 1 MeV. See Ris, H 1981 Stereoscopic Electron Microscopy of chromosomes. Meth Cell Biol 22:77-96; Ris, H 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:229-246
DOI: 10.6075/j0h132bw
title: CIL:56103, Homo sapiens. In Cell Image Library

description: Scan 09_C_ED_D -- 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
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.
DOI: 10.6075/j0668bt9
title: CIL:35617, Xenopus laevis, tissue culture cell. In Cell Image Library

description: Phase contrast images were captured at 15 sec intervals using a Zeiss 200 inverted microscope with 63x 1.4NA objective lens.
description: 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: Time lapse movie of mitosis in Xenopus laevis tissue culture cell. The sequence illustrates the requirement for all chromosomes to be aligned on the metaphase plate before anaphase is initiated.
DOI: 10.6075/j0tq60h4
title: CIL:35610, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film; Print of negative scanned for Photoshop
Data qualification: Processed
description: Quick-freeze deep-etch of an ampulla. The P-fracture face has numerous IMPs. The microtubular ribbon now forms two bands next to this ampulla. The ribbons will split into additional bands as they pass on to and around the collecting canal. TEM taken on 1/14/95 by R. Allen with Zeiss 10A operating at 80kV. Neg. 19,800X. Bar = 0.2µm. A print of the negative was scanned and processed in Photoshop. This image is best used for qualitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0vq32pc
title: CIL:35625, 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; 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.
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.
DOI: 10.6075/j05x27x2
title: CIL:35558, Cricetulus griseus, ovary. In Cell Image Library

description: Colcemid-arrested cells were swollen in hypotonic 75mM KCl, fixed with 4% HCOH, post-fixed with OsO4, embedded in plastic, and 'thick' 0.25 micron sections prepared. Sections were recorded using the Wisconsin HVEM at 1 MeV. See Ris (1978) Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:229-246; Ris (1981) Stereoscopic electron microscopy of chromosomes. Meth Cell Biol 22:77-96.
description: Preparation: formaldehyde fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide
Processing history: unprocessed raw data
description: Metaphase-arrested CHO cells were swollen in 75 mM KCL, fixed with formaldehyde, post-fixed with OsO4, embedded, and 0.25 micron sections examined by High Voltage EM. Seen is a longitudinal section through a chromatid pair with kinetochore elements. This image recorded with a specimen tilt of 40 degrees is part of a grouped tilt series ranging from 20 degrees to 75 degrees. Pairs providing oblique stereo views of chromosome organization.
DOI: 10.6075/j05m6510
title: CIL:39337, Euplotes sp., 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
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: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol, and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness.
description: At this level of the buccal cavity the opening into the cytopharynx is not seen. Pharyngeal vesicles accumulate at the ends of the cytopharyngeal lamellae and are present under the basal bodies of the membranelles. The alveolar sacs are still present at this level. TEM taken on 7/29/67 by R. Allen with Philips 200 operating at 60kV. Neg. 9,000X. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0hx1c0b
title: CIL:39308, Paramecium multimicronucleatum, 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; uranyl salt; lead salt; osmium tetroxide
Processing history: recorded image; film
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Striated band spanning the base of a longitudinal ridge (kinetodesmal fibers are seen in the ridge in cross section). The epiplasm appears absent from the top of the ridge or is replaced by two thickenings connected by thin filaments. Observing from outside the cell looking from the posterior toward the anterior direction. TEM taken on 12/9/70 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 37,750X.
description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j08p5z43
title: CIL:39332. In Cell Image Library
DOI: 10.6075/j0gm86mk
title: CIL:39327, Vorticella convallaria, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: 11 micrographs are views of a serially-sectioned contracted Vorticella convallaria cell that show the main features of this cell. This figure shows 3 food vacuoles (of a total of about 15 in the cell) containing bacteria and part of a trochal band of basal bodies that surrounds the aboral scopular zone where the stalk originates. TEM taken on 4/2/71 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 3,150X. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. 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
Data qualification: Raw
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/).
DOI: 10.6075/j04f1pcr
title: CIL:39326, Vorticella microstoma, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: This freeze fracture view of the pellicle of V. microstoma near the aboral end of the zooid shows the region where the width of each circumferential alveolus is narrower and thus the strings of fractured pits are closer together. In this case the E-fracture face of the outer alveolar membrane is shown which has fewer IMPs than the P-face of the outer alveolar membrane. Here the connections are indentations rather than fractured necks. In a few areas the P-fracture face of the plasma membrane is viewed where it was pinched into the folds between rings that surround the cell. The plasma membrane demonstrates the large number of prominent IMPs on this face of the plasma membrane. TEM taken on 11/11/75 by R. Allen with JEM 100B. Neg. 21,578X. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).