cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j02z14pq
title: CIL:9696, Coleps hirtus, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: An image image of the multiple membrane systems at the cortex of ciliates. Thickened alveolar densities partially coat the alveolar membrane within the alveoli which underlie the plasma membrane of ciliates. The densities are seen particularly along the inner membrane at its corners with the septa. Fibrous systems lie within the cytoplasm next to these densities. Cross sections of four cilia are also seen. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. TEM taken on 5/28/69 by R. Allen with Philips 300 operating at 60kV. Neg. 14,800X. 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:9017) is available 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
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 of negative scanned for Photoshop.
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j07d2t7k
title: CIL:9686, Xenopus laevis. In Cell Image Library

description: Preparation: methanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: YO-PRO-1; Alexa Fluor 647; labeled primary antibody
Processing history: unprocessed raw data
description: Frog (Xenopus laevis) egg arrested in metaphase of mitosis. Note the tiny metaphase spindle on the top left of the egg. 

Eggs were fixed in 90% MeOH; 10% (H20 500mM EGTA) and stained for DNA with YoPro1 (green) and tubulin (red) with antibody B-5-1-2 directly labeled with Alexa 647. A single z slice was collected with a Zeiss LSM 710 using a 10 X 0.3NA objective. Lasers were 488 (DNA stain) and 633 (Tubulin stain).
DOI: 10.6075/j0765dfc
title: CIL:9301, Rana catesbeiana, barrier epithelial cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: uranyl salt; lead salt; osmium tetroxide
Processing history: unprocessed raw data
description: This group of micrographs illustrate the ultrastructural characteristics of the middle layer of the three meningeal layers that cover the central nervous system The arachnoid cells contain abundant intermediate filaments that occupy a substantial volume of the cytoplasm. In some cells the intermediate filaments are organized into numerous coils of relatively uniform size and orientation. The coils appear to stack in loose hexagonal arrays. The plasma membrane of these cells has many caveolae. Adjacent arachnoid cells are connected by large desmosomes.

Images were recorded using a Philips EM301 TEM at 80 kv. Original glass plates were scanned and digitized using an Epson V750 flatbed scanner with a step size of 15 micrometers.

This group of images complement those published in the reference below.

Reference: Michaels, JE, Tornheim, PA. Cell Tissue Res. 236:693-697 (1984).
DOI: 10.6075/j0b56hvz
title: CIL:9253, Coleps hirtus, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: A high resolution of some tubules near a contractile vacuole that appear to be decorated with pegs similar to the spongiome of the CV of Paramecium. In Paramecium these pegs are known to be V-type proton pumps (V-ATPases). Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. TEM taken on 3/2/69 by R. Allen with Philips 300. Neg. 12,500X. The raw film was scanned with an Epson Perfection V750 Pro. This high resolution image is available for quantitative analysis. Additional information is available at (http://www5.pbrc.hawaii.edu/allen/).
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: film; unprocessed raw data
DOI: 10.6075/j0rj4hn1
title: CIL:9512, Xenopus laevis. In Cell Image Library

description: Frog (Xenopus laevis) egg arrested in metaphase of mitosis. Note the tiny metaphase spindle on the top left of the egg. 

Eggs were fixed in 90% MeOH; 10% (H20 500mM EGTA) and stained for DNA with YoPro1 (green) and tubulin (red) with antibody B-5-1-2 directly labeled with Alexa 647. A single z slice was collected with a Zeiss LSM 710 using a 10 X 0.3NA objective. Lasers were 488 (DNA stain) and 633 (Tubulin stain).
description: Preparation: methanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: YO-PRO-1; Alexa Fluor 647; labeled primary antibody
Processing history: unprocessed raw data
DOI: 10.6075/j0fn15bz
title: CIL:9254, Coleps hirtus, 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; unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: This high resolution micrograph may show important features involved in calcareous plate formation within the alveoli that underlie the plasma membrane in Coleps. Densities are seen on the inner alveolar membrane at its corners with septa. These densities are not known at this time in other ciliates and may be involved in calcareous platelet formation within the alveoli or in stabilizing the surface shape. Filamentous material fills the cytosolic space between two densities. Rough endoplasmic reticulum bears prominent ribosomes. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. TEM taken on 3/4/69 by R. Allen with Philips 300 operating at 60kV. Neg. 39,900X. The raw film was scanned with an Epson Perfection V750 Pro. This high resolution image is suitable for quantitative analysis.

Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0mw2fqj
title: CIL:49801, Primary human small airway epithelial cells immortalized with telomerase. In Cell Image Library

description: Primary human small airway epithelial cells in interphase state were fixed with 2.5% glutaraldehyde, 5 mM CaCl<sub>2</sub> in 0.1 M sodium cacodylate buffer (pH 7.4). Cells were stained with 10 µM DRAQ5, and photo-oxidized at 620 ± 30 nm for 8 minutes. Cells were post-fixed with 2% osmium tetroxide, 2 mM CaCl<sub>2</sub>, 1.5% potassium ferrocyanide in 0.15 M sodium cacodylate buffer (pH 7.4). Samples were ethanol dehydrated, embedded in Durcupan epoxy resin and sectioned to 250 nm thickness and mounted on copper slot grid. 5 nm and 10 nm colloidal gold particles were deposited on the grid as fiducial markers. 8-tilt EM tomography was collected on a 300 kV FEI Titan Krios using a 4K by 4K Gatan Ultrascan CCD camera at 1 degree increment for each tilt series from -60° to +60°. The entire set of EMT images was aligned and reconstructed using the Transform-based Tracking, Bundle adjustment, and Reconstruction (TXBR) package. The data has a voxel size of 1.28 nm.
description: Multi-tilt EM tomogram of primary human small airway epithelial cell (SAEC) in interphase state. The tomogram refers to the SAEC in Figure 4 of the published manuscript: 
http://science.sciencemag.org/content/357/6349/eaag0025
description: Preparation: Glutaraldehyde fixed cells, photo-oxidation of DRAQ5 in the presence of DAB solution to induce DAB polymerization and subsequent staining with osmium tetroxide
Relation to intact cell: semi-thin section ~250 nm
Item type: recorded image
Imaging mode: 8-tilt EM tomography
Parameter imaged: electron density
Source of contrast: Osmium tetroxide staining of DAB polymers catalyzed by photo-oxidation of DRAQ5 stained cells in the presence of DAB solution
DOI: 10.6075/j0d7990q
title: CIL:49453, Mus musculus, C57BL/6, central nervous system. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; differences in adsorption or binding of stain
Visualization methods: primary antibody plus labeled secondary antibody; Hoechst 33342
description: Mouse brain was perfused with 4% paraformaldehyde, sectioned through the hippocampus in the coronal plane on a vibratome (100 µm). The section was immunostained with RIβ and RIIβ primary antibodies. Secondary antibodies: Alexa Fluor 488 Donkey anti rabbit (green) and CY3 Donkey anti sheep (red). Images were acquired with a FluoView 1000 (Olympus Center Valley, PA,USA) using 20X objective and a high-precision motorized stage to collect the large scale mosaics. The specimen was excited sequentially with a laser at two different wavelengths: 488nm and 561nm. The boundaries (in x, y, and z) of the tissue section were defined using the Multi-Area Time Lapse function of ASW 1.7c microscope operating-software provided by Olympus (Olympus, Center Valley, PA, USA). The software automatically generates a list of 3D stage positions covering the volume of interest, which are computed using the dimensions of a single image in microns, degree of overlap between adjacent images and z-step size. Individual image tiles were 1024 × 1024 with a pixel dimension of 0.62 μm; overlap between two adjacent images (x-y) was 10% and the z-step was ~0.5 mm/section; there is no overlap in z. image normalization was performed using ImageJ.

Reconstruction Data File
Montage of a mouse coronal section triple labeled for Hoescht stain (blue), PKA RIβ regulatory subunit (red), and PKA RIIβ regulatory subunit (green).
Reconstruction Data Files, mosaic reconstructed with 10% overlap; image normalization performed using imageJ.
description: High-resolution, large-scale mosaic image for a full coronal mouse tissue showing global views of different brain regions, as well as cellular and subcellular details, identified distinct localization of PKA RIβ and RIIβ regulatory subunits. 
Triple labeled for Nuclei (Hoescht stain, blue), RIβ (cy3, red) and RIIβ (Alexa 488, green). This image is a maximum projection of the Z-stack through the tissue, and has been downsampled from the raw data image, which can be accessed using the link provided to the Cell Image Library.
DOI: 10.6075/j0n58jz8
title: CIL:49759, Lesional skin. In Cell Image Library

description: Two mm skin were fixed in 2% glutaraldehyde in 0.1 M sodium cacodylate buffer pH 7.4 washed in 0.1 M sodium cacodylate buffer and postfixed in 1% osmiumtetroxide and 1.5% potassiumferrocyanide. Samples were dehydrated, embedded in epon, and sectioned. Ultrathin sections (70 nm) were positioned on single slot holders A600 Nickel supported by Formvar and contrasted with 2% uranylacetate (methanol) followed by Reynolds lead citrate. Acquisition was performed using a Zeiss supra 55 EM (Oberkochen, Germany) with ATLAS software developed by Fibics (Ottawa, Ontario, Canada). Samples were recorded at 2.5 nm pixel size. Scans were stitched, and raw data sets were rendered as HTML files using ATLAS VE viewer software. data sets are orientated such that the epidermis/superficial layers are facing up.
description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: ultrathin section
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: electron density
description: High-resolution montage of a thin section of Healthy human skin, including part of the dermis and all epidermal layers. This image is a montage of 32 images and a series of 10 datasets as published: 
 
http://www.jidonline.org/article/S0022-202X(15)37322-X/fulltext 
 
http://www.nanotomy.org/OA/Sokol2015JID/index.html
DOI: 10.6075/j01z4305
title: CIL:49751, Lesional skin. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: ultrathin section
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: electron density
description: Two mm skin were fixed in 2% glutaraldehyde in 0.1 M sodium cacodylate buffer pH 7.4 washed in 0.1 M sodium cacodylate buffer and postfixed in 1% osmiumtetroxide and 1.5% potassiumferrocyanide. Samples were dehydrated, embedded in epon, and sectioned. Ultrathin sections (70 nm) were positioned on single slot holders A600 Nickel supported by Formvar and contrasted with 2% uranylacetate (methanol) followed by Reynolds lead citrate. Acquisition was performed using a Zeiss supra 55 EM (Oberkochen, Germany) with ATLAS software developed by Fibics (Ottawa, Ontario, Canada). Samples were recorded at 2.5 nm pixel size. Scans were stitched, and raw data sets were rendered as HTML files using ATLAS VE viewer software. data sets are orientated such that the epidermis/superficial layers are facing up.
description: High-resolution montage of a thin section of Healthy human skin, including part of the dermis and all epidermal layers. This image is a montage of 32 images and a series of 10 datasets as published: 

http://www.jidonline.org/article/S0022-202X(15)37322-X/fulltext 
 
http://www.nanotomy.org/OA/Sokol2015JID/index.html
DOI: 10.6075/j0pv6hxv
title: CIL:49194, Homo sapiens. In Cell Image Library

description: Plate 24303 - Phenotypic profiling attempts to summarize multiparametric, feature-based analysis of cellular phenotypes of each sample so that similarities between profiles reflect similarities between samples. This image set provides a basis for testing image-based profiling methods wrt. to their ability to distinguish the effects of small molecules. The images are of U2OS cells treated with each of 1600 known bioactive compounds and labeled with six labels that characterize seven organelles (the cell-painting assay). This experiment consists of 375 plates in 384-well format, for a data set comprised of 988,994 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale image file, so there are approximately 5 million image files in 16-bit TIFF format.
description: Gustafsdottir et al. (doi:10.1371/journal.pone.0080999) have developed a multiplex cytological profiling assay that "paints the cell" with as many fluorescent markers as possible without compromising our ability to extract rich, quantitative profiles in high throughput. The assay detects seven major cellular components. In a pilot screen of bioactive compounds, the assay detected a range of cellular phenotypes and it clustered compounds with similar annotated protein targets or chemical structure based on cytological profiles. The results demonstrate that the assay captures subtle patterns in the combination of morphological labels, thereby detecting the effects of chemical compounds even though their targets are not stained directly. This image-based assay provides an unbiased approach to characterize compound- and disease-associated cell states to support future probe discovery. Using the cell-painting assay, the Broad Institute has assembled a reference dataset of profiles for U2OS osteosarcoma cells treated with ~30,000 compounds. The compound collection includes DOS-derived compounds (20,000), as well as chemically diverse MLI compounds with biologically diverse performance identified through analysis of PubChem (10,000), and known bioactive compounds to serve as landmarks (2,500). The DOS compounds consist of structurally diverse and stereochemically rich compounds with structures distinct from the current MLSMR. The compound collection also includes 267 distinct compounds nominated by MLPCN Centers from projects for which the Centers would like to identify new chemical series with similar activities. The experiment consists of 375 microtiter plates. Each plate has 384 wells. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale 16-bit TIFF image file.

The experiment consists of 375 microtiter plates. Each plate has 384 wells. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale 16-bit TIFF image file.
DOI: 10.6075/j0tb15fm
title: CIL:49754, Normal human skin. In Cell Image Library

description: High-resolution montage of a thin section of Healthy human skin, including part of the dermis and all epidermal layers. This image is a montage of 32 images and a series of 10 datasets as published: 
 
http://www.jidonline.org/article/S0022-202X(15)37322-X/fulltext 
 
http://www.nanotomy.org/OA/Sokol2015JID/index.html
description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: ultrathin section
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: electron density
description: Two mm skin were fixed in 2% glutaraldehyde in 0.1 M sodium cacodylate buffer pH 7.4 washed in 0.1 M sodium cacodylate buffer and postfixed in 1% osmiumtetroxide and 1.5% potassiumferrocyanide. Samples were dehydrated, embedded in epon, and sectioned. Ultrathin sections (70 nm) were positioned on single slot holders A600 Nickel supported by Formvar and contrasted with 2% uranylacetate (methanol) followed by Reynolds lead citrate. Acquisition was performed using a Zeiss supra 55 EM (Oberkochen, Germany) with ATLAS software developed by Fibics (Ottawa, Ontario, Canada). Samples were recorded at 2.5 nm pixel size. Scans were stitched, and raw data sets were rendered as HTML files using ATLAS VE viewer software. data sets are orientated such that the epidermis/superficial layers are facing up.
DOI: 10.6075/j03t9fsr
title: CIL:49753, Non-lesional skin. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: ultrathin section
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: electron density
description: High-resolution montage of a thin section of Healthy human skin, including part of the dermis and all epidermal layers. This image is a montage of 32 images and a series of 10 datasets as published: 
 
http://www.jidonline.org/article/S0022-202X(15)37322-X/fulltext 
 
http://www.nanotomy.org/OA/Sokol2015JID/index.html
description: Two mm skin were fixed in 2% glutaraldehyde in 0.1 M sodium cacodylate buffer pH 7.4 washed in 0.1 M sodium cacodylate buffer and postfixed in 1% osmiumtetroxide and 1.5% potassiumferrocyanide. Samples were dehydrated, embedded in epon, and sectioned. Ultrathin sections (70 nm) were positioned on single slot holders A600 Nickel supported by Formvar and contrasted with 2% uranylacetate (methanol) followed by Reynolds lead citrate. Acquisition was performed using a Zeiss supra 55 EM (Oberkochen, Germany) with ATLAS software developed by Fibics (Ottawa, Ontario, Canada). Samples were recorded at 2.5 nm pixel size. Scans were stitched, and raw data sets were rendered as HTML files using ATLAS VE viewer software. data sets are orientated such that the epidermis/superficial layers are facing up.
DOI: 10.6075/j0cz35q4
title: CIL:49758, Normal human skin. In Cell Image Library

description: Two mm skin were fixed in 2% glutaraldehyde in 0.1 M sodium cacodylate buffer pH 7.4 washed in 0.1 M sodium cacodylate buffer and postfixed in 1% osmiumtetroxide and 1.5% potassiumferrocyanide. Samples were dehydrated, embedded in epon, and sectioned. Ultrathin sections (70 nm) were positioned on single slot holders A600 Nickel supported by Formvar and contrasted with 2% uranylacetate (methanol) followed by Reynolds lead citrate. Acquisition was performed using a Zeiss supra 55 EM (Oberkochen, Germany) with ATLAS software developed by Fibics (Ottawa, Ontario, Canada). Samples were recorded at 2.5 nm pixel size. Scans were stitched, and raw data sets were rendered as HTML files using ATLAS VE viewer software. data sets are orientated such that the epidermis/superficial layers are facing up.
description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: ultrathin section
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: electron density
description: High-resolution montage of a thin section of Healthy human skin, including part of the dermis and all epidermal layers. This image is a montage of 32 images and a series of 10 datasets as published: 
 
http://www.jidonline.org/article/S0022-202X(15)37322-X/fulltext 
 
http://www.nanotomy.org/OA/Sokol2015JID/index.html
DOI: 10.6075/j0k64gnm
title: CIL:49701, Normal human skin. In Cell Image Library

description: Two mm skin were fixed in 2% glutaraldehyde in 0.1 M sodium cacodylate buffer pH 7.4 washed in 0.1 M sodium cacodylate buffer and postfixed in 1% osmiumtetroxide and 1.5% potassiumferrocyanide. Samples were dehydrated,
embedded in epon, and sectioned. Ultrathin sections (70 nm) were positioned on single slot holders A600 Nickel supported by Formvar and contrasted with 2% uranylacetate (methanol) followed by Reynolds lead citrate. Acquisition was performed using a Zeiss supra 55 EM (Oberkochen, Germany) with ATLAS software developed by Fibics (Ottawa, Ontario, Canada).
 
Samples were recorded at 2.5 nm pixel size. Scans were stitched, and raw data sets were rendered as HTML files using ATLAS VE viewer software. data sets are orientated such that the epidermis/superficial layers are facing up.
description: High-resolution montage of a thin section of Healthy human skin, including part of the dermis and all epidermal layers. This image is a montage of 32 images and a series of 10 datasets as published:

http://www.jidonline.org/article/S0022-202X(15)37322-X/fulltext

http://www.nanotomy.org/OA/Sokol2015JID/index.html
description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: ultrathin section
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Visualization methods: electron density