cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0dr2vmx
title: CIL:40226, Mus musculus, astrocyte of the hippocampus. In Cell Image Library

description: Single computed slice through a tomographic reconstruction of the cell body of a protoplasmic astrocyte in a 0.5 um thick section from the hippocampus of a 1 month old male mouse, imaged with intermediate voltage electron microscopy. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. The reconstruction is the 8th in a series of 26 serial reconstructions through the cell soma. All 26 images can be found in this image group within the Cell Library, and the complete reconstruction can be viewed in the Cell centered database, accession # 7503.
description: Preparation: glutaraldehyde fixed tissue; formaldehyde fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: osmium tetroxide; lead salt
Data qualification: Processed
description: Detailed methods can be found at the CCDB link provided. Briefly, one month old male mouse (C57BL/6NHsd) was perfused with Ringer's solution for 2 minutes followed by 2% glutaraldehyde and 2% paraformaldehyde in 0.15M sodium cacodylate buffer, pH 7.4. Further dissection of tissue was followed with postfixation using 1% OsO4, additional staining using 2% uranyl acetate, processed for embedding in durcupan ACM resin, and sectioned at a thickness of 5µm thick. Serial tomograms were produced from single tilt images using a JEOL4000, with 8k x 8k CCD camera, 5000X, 400.0 keV).
DOI: 10.6075/j0b85777
title: CIL:13183, Haemanthus katharinae, endosperm. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: elastic scattering of electrons
Visualization methods: uranyl salt
Processing history: unprocessed raw data
description: Dividing cells from the liquid endosperm of the lily Haemanthus katherinae were fixed with paraformaldehye, embedded in epoxy, 0.5 micrometer sections prepared, and stained with uranyl magnesium acetate. Images were obtained with the Wisconsin high voltage TEM at 1MEV. For this micrograph of chromosomes at anaphase, the grid was tilted to 40 degrees. A similar micrograph tilted to 60 degrees is grouped with this image, making a stereo pair that provides an oblique 3D view.
DOI: 10.6075/j01j993r
title: CIL:38665, Rattus rattus, glandular epithelial cell, milk secreting cell, mammary alveolar cell. In Cell Image Library

description: Immunoelectron microscopy of mammary gland tissue from lactating rats investigating potential structural interactions between mature lipid droplets and elements of the trans-Golgi network, identified by TGN38 (a transmembrane trans-Golgi protein; larger gold particles) and cation-dependent mannose-6-phosphate receptor (an integral membrane protein that localizes to the trans-Golgi
 reticulum, endosomes, and the plasma membrane; smaller gold particles) staining. Note that trans‚ÄêGolgi cisternae in lactating mammary cells contain large amounts of casein and other milk proteins and are grossly expanded due to the osmolarity of the secreted fluid.
description: Preparation: cryostat-sectioned tissue; formaldehyde fixed tissue; embedded tissue; methylcellulose embedded
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain; distribution of a specific protein
Visualization methods: gold; uranyl salt; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Tissue was processed for immunoelectron microscopy using a modified Tokuyasu method. Briefly, minced tissue was fixed in 4% paraformaldehyde containing 5% sucrose and 100 mM HEPES and infiltrated with PBS containing 2.1 M sucrose over 10 h, with repeated solution changes. Fixed tissue was transferred to an aluminum cryosectioning stub (Ted Pella, Inc., Redding, CA) and immediately frozen in liquid nitrogen. Semithin (90 nm) cryosections were cut at -110C with an UltraCut UCT/FCS cryomicrotome (Leica), using a diamond knife (Diatome) and transferred to a Formvar-coated, carbon-coated, glow-discharged 100-mesh copper-rhodium electron microscopy grid. Following blocking of nonspecific antibody binding sites with 10% calf serum in PBS, the sections were labeled by sequential incubation with antibodies to cation-dependent mannose-6-phosphate receptor (rabbit) and TGN38 (mouse monoclonal 2F7) and colloidal gold-conjugated secondary antibodies (10 nm anti-rabbit, 15 nm anti-mouse; Ted Pella Inc., Redding, CA) and then negatively stained and embedded with 1% uranyl acetate, 1% methylcellulose in distilled water. Samples were viewed in a Philips CM10 electron microscope, and images were collected digitally. Magnification 11,500 X. See Ladinsky and Howell (2007) for more information on methods used.
DOI: 10.6075/j03r0sxk
title: CIL:32110, Homo sapiens, osteocarcenoma. In Cell Image Library

description: The images constitute one row of a 348 well plate. The dose curve consists of 11 dose points and one control. Each concentration is duplicated in adjacent wells. Each well has three fields.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: plate reader
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; distribution of DNA
Visualization methods: EGFP
Processing history: unprocessed raw data
description: This image set is of Transfluor assay where an orphan GPCR (G-protein coupled receptor) is stably integrated into a beta-arrestin GFP (green) expressing U2OS cell line also showing nucleus (red). After one hour incubation with a compound, the cells were quenched with fixative (formaldehyde) and the plate was read on Cellomics ArrayScan HCS Reader using the GPCR Bioapplication. Negative results are a more uniform distribution of GFP throughout the cytoplasm and positive results are a peri-nuclear localization.
Recommended attribution: "We used the SBS Roche Transfluor image set provided by Ilya Ravkin and available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
Analysis of the data set can be downloaded from http://www.broadinstitute.org/bbbc/sbs_roche_transfluor.html
DOI: 10.6075/j0x929gp
title: CIL:13187, Haemanthus katharinae, endosperm. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: elastic scattering of electrons
Visualization methods: uranyl salt
Processing history: unprocessed raw data
description: Dividing cells from the liquid endosperm of the lily Haemanthus katherinae were fixed with paraformaldehye, embedded in epoxy, and 1.0 micrometer sections prepared. Images were obtained with the Wisconsin high voltage TEM at 1MEV. For this micrograph of chromosomes at anaphase, the grid was tilted to 40 degrees. A similar micrograph tilted to 60 degrees is grouped with this image, making a stereo pair that provides an oblique 3D view.
DOI: 10.6075/j0rn36k2
title: CIL:13160, Homo sapiens, keratinocyte, epidermal cell. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
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: custom-made smoothing, sharpening, and convolution filters using MetaMorph software
Data qualification: Processed
description: Topographical regulation of keratinocyte migration. 2D, 3D, and 1D fibrillar migration of human epidermal keratinocytes. 2D matrices were constructed by uniform coating with extracellular matrix (ECM). 3D surfaces were constructed according to Science. 294: 1708–1712 (2001). 1D surfaces were made by using a 2 photon confocal microscope to pattern a polyvinyl alchohol (PVA) coated coverslip. Movie is video 4 from JCB 2009, 184:481-490
description: Following gluteraldehyde quenching, ECM proteins were absorbed onto the PVA surface. Videos were recorded on a Axiovert 135TV (Carl Zeiss, Inc.) with a charge-coupled device camera (ORCA II ER; Hamamatsu Photonics). MetaMorph imaging software was used to acquire images and control all hardware. A custom environmental chamber (Lucite) enclosed both time-lapse and TIRF microscopes and maintained cells at 37°C with 10% CO2. Images were collected every 4 min and shown at 15 frames per second.
DOI: 10.6075/j0k35sx8
title: CIL:1316, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Rabbit psoas skeletal muscle fibers were held at constant length and rigor induced by immersion in glycerol. The fibers were quick-frozen by contact with a liquid helium- cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 24 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

Images were recorded on Kodak 4489 film at 100,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:914.
description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
DOI: 10.6075/j0tt4png
title: CIL:13159, Mus musculus, fibroblast. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
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: custom-made smoothing, sharpening, and convolution filters using MetaMorph software
Data qualification: Processed
description: Videos were recorded on a Axiovert 135TV (Carl Zeiss, Inc.) with a charge-coupled device camera (ORCA II ER; Hamamatsu Photonics). MetaMorph imaging software was used to acquire images and control all hardware. A custom environmental chamber (Lucite) enclosed both time-lapse and TIRF microscopes and maintained cells at 37°C with 10% CO2. Images were collected every 4 min and shown at 15 frames per second.
description: Multiple NIH-3T3 fibroblasts undergoing 1D fibrillar migration. Cells were plated on polyvinyl alchohol (PVA) coated coverslips that had been patterned by ablation with a 2 photon confocal microscope. Following gluteraldehyde quenching, extracellular matrix proteins were absorbed onto the PVA surface. Movie is video 3 from JCB 2009, 184:481-490
DOI: 10.6075/j0pr7v41
title: CIL:13158, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: The proximal end of the basal body is sometimes the origin of other single microtubules or bundles of microtubules that extend deeper into the cell's endoplasm. These guide trichocysts, tip first, to the cell surface and spent vacuoles to the cytoproct. Septal pores connect adjacent alveolar sacs. TEM taken on 1/12/73 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 12,350X. Bar = 0.5µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. An unprocessed, high resolution version of this image (CIL:12070) is in the library and available for quantitative analysis. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed
DOI: 10.6075/j0j38rpj
title: CIL:13154, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: A tangential section through the cell's surface show the pairs of basal bodies in cross section. The ends of kinetodesmal fibers point anteriorly in the cell, the postciliary ribbons arise from the posterior right side of the posterior basal body of a pair and transverse ribbons arise from the left side of both basal bodies of a pair. The more anterior basal body of a pair is linked to the posterior basal body by a striated fiber and to the adjacent kinetodesmal fiber by a short filamentous connection (arrowhead). Parasomal sacs, infraciliary lattice, striated band, and trichocyst tips are evident. TEM taken on 1/12/73 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 14,900X. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. An unprocessed, high resolution version of this image (CIL:12031) is in the library and available for quantitative analysis. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed
DOI: 10.6075/j0nv9hch
title: CIL:13153, Micrasterias denticulata. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: whole mounted tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: electron density
Visualization methods: shadowing and plating
Data qualification: Raw;spatialmeasurements
description: Micrograph illustrating the general preservation of the cytoplasm in a Micrasterias cell stabilized by ultrarapid freezing. P-face of RER membranes depicting several spiral imprints of polysomes. The substructure of the imprint ridge presumably reflects imprints of the individual ribosomes. 

Technical details:
Cultures of Micrasterias denticulata were obtained from the Algal Culture Collection, University of Indiana (Cat. No . LB558) . Cells were grown in Waris medium MS at 18°C on a 15/9-h, fight-dark cycle. For each experiment, cells about halfway through the dark cycle were placed in fresh medium in continuous light. This treatment stimulated many cells to divide ~25 h later. Healthy, growing cells were then selected with a dissecting microscope and placed in a separate Petri dish containing growth medium buffered with 2 mM 2(N-morpholino)-ethane sulfonic acid adjusted to pH 6.0. Cells at the desired stage of development were then placed in another dish containing 1% glutaraldehyde in buffered medium and fixed for 20 min. Gold double-replica supports (Balzers High Vacuum Corp ., Santa Ana, Calif.) were coated with a thin layer of yeast paste. Fixed cells were placed on one support and the second support was placed on top. This "sandwich" was plunged into liquid propane near its melting point and stored in liquid nitrogen. Cells were ultrarapidly frozen using a propane-jet device of the type described by Miiller et al (see reference). Samples were prepared as described above, with the following exceptions: cells were frozen directly in growth medium, without prior fixation; the gold supports used had been hollowed out, leaving a metal thickness of 127 micron and the propane-jet device was used. Samples were fractured and replicated using a Balzers double-replica device in a Balzers BA 360 freeze-etch unit. Fracturing was done at -110°C. The yeast paste allowed recovery of large, intact replicas; these were cleaned in commercial bleach and 70% sulfuric acid at 60°C. Replicas were examined in a JEOL EM 100C at 33,000X magnification.

Image reference: PMID: 7364870.
Ribosome binding sites visualized on freeze-fractured membranes of the rough endoplasmic reticulum. Giddings TH Jr, Staehelin LA. J Cell Biol. 1980 Apr;85(1):147-52.
DOI: 10.6075/j0n58kkr
title: CIL:13152, Micrasterias denticulata. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: whole mounted tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: electron density
Visualization methods: shadowing and plating
Data qualification: Raw;spatialmeasurements
description: The P-face of the plasma membrane of a semicell engaged in the synthesis of the secondary wall. Hexagonal arrays of rosettes of varying size and shape can be observed. The large circular indentations may correspond to forming slime secretion pore complexes. Propanejet freezing.

Technical details:
Cultures of Micrasterias denticulata were obtained from the Algal Culture Collection, University of Indiana (Cat. No . LB558) . Cells were grown in Waris medium MS at 18°C on a 15/9-h, fight-dark cycle. For each experiment, cells about halfway through the dark cycle were placed in fresh medium in continuous light. This treatment stimulated many cells to divide ~25 h later. Healthy, growing cells were then selected with a dissecting microscope and placed in a separate Petri dish containing growth medium buffered with 2 mM 2(N-morpholino)-ethane sulfonic acid adjusted to pH 6.0. Cells at the desired stage of development were then placed in another dish containing 1% glutaraldehyde in buffered medium and fixed for 20 min. Gold double-replica supports (Balzers High Vacuum Corp ., Santa Ana, Calif.) were coated with a thin layer of yeast paste. Fixed cells were placed on one support and the second support was placed on top. This "sandwich" was plunged into liquid propane near its melting point and stored in liquid nitrogen. Cells were ultrarapidly frozen using a propane-jet device of the type described by Miiller et al (see reference). Samples were prepared as described above, with the following exceptions: cells were frozen directly in growth medium, without prior fixation; the gold supports used had been hollowed out, leaving a metal thickness of 127 micron and the propane-jet device was used. Samples were fractured and replicated using a Balzers double-replica device in a Balzers BA 360 freeze-etch unit. Fracturing was done at -110°C. The yeast paste allowed recovery of large, intact replicas; these were cleaned in commercial bleach and 70% sulfuric acid at 60°C. Replicas were examined in a JEOL EM 100C at 50,000X magnification.

Image reference: PMID: 7189756. 
Visualization of particle complexes in the plasma membrane of Micrasterias denticulata associated with the formation of cellulose fibrils in primary and secondary cell walls. Giddings TH Jr, Brower DL, Staehelin LA. J. Cell Biol. 1980 Feb;84(2):327-39.
DOI: 10.6075/j0tt4q45
title: CIL:13151, Micrasterias denticulata. In Cell Image Library

description: The P-face of the plasma membrane of a semicell engaged in the synthesis of the secondary wall. Hexagonal arrays of rosettes of varying size and shape can be observed. The large circular indentations may correspond to forming slime secretion pore complexes. Propanejet freezing.

Technical details:
Cultures of Micrasterias denticulata were obtained from the Algal Culture Collection, University of Indiana (Cat. No . LB558) . Cells were grown in Waris medium MS at 18°C on a 15/9-h, fight-dark cycle. For each experiment, cells about halfway through the dark cycle were placed in fresh medium in continuous light. This treatment stimulated many cells to divide ~25 h later. Healthy, growing cells were then selected with a dissecting microscope and placed in a separate Petri dish containing growth medium buffered with 2 mM 2(N-morpholino)-ethane sulfonic acid adjusted to pH 6.0. Cells at the desired stage of development were then placed in another dish containing 1% glutaraldehyde in buffered medium and fixed for 20 min. Gold double-replica supports (Balzers High Vacuum Corp ., Santa Ana, Calif.) were coated with a thin layer of yeast paste. Fixed cells were placed on one support and the second support was placed on top. This "sandwich" was plunged into liquid propane near its melting point and stored in liquid nitrogen. Cells were ultrarapidly frozen using a propane-jet device of the type described by Miiller et al (see reference). Samples were prepared as described above, with the following exceptions: cells were frozen directly in growth medium, without prior fixation; the gold supports used had been hollowed out, leaving a metal thickness of 127 micron and the propane-jet device was used. Samples were fractured and replicated using a Balzers double-replica device in a Balzers BA 360 freeze-etch unit. Fracturing was done at -110°C. The yeast paste allowed recovery of large, intact replicas; these were cleaned in commercial bleach and 70% sulfuric acid at 60°C. Replicas were examined in a JEOL EM 100C at 33,000X magnification.

Image reference: PMID: 7189756. 
Visualization of particle complexes in the plasma membrane of Micrasterias denticulata associated with the formation of cellulose fibrils in primary and secondary cell walls. Giddings TH Jr, Brower DL, Staehelin LA. J. Cell Biol. 1980 Feb;84(2):327-39.
description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: whole mounted tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: electron density
Visualization methods: shadowing and plating
Data qualification: Raw;spatialmeasurements