cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0rj4hgs
title: CIL:36280, Vorticella convallaria, 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; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed
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: Vorticella convallaria has a contractile stalk that arises from the aboral pole of the cell. The myonemes from the body converge at this pole and pass into the stalk to form a large contractile bundle called the spasmoneme. When contracted the stalk coils into a helix. The spasmoneme is partially encased in an extension of the pellicle and a thin layer of cytosol that is enclosed with plasma membrane. An additional secreted sheath surrounds the stalk. TEM taken on 4/6/72 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 7,500X. Bar = 1µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. There is a high resolution version of this image in the library (CIL:39517) which is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0n58k3g
title: CIL:13700, Chlorocebus aethiops. In Cell Image Library

description: This is one of a group of four images in Figure S5 in Apaja et al., JCB 2010, that support the conclusion that the WT vasopressin type2 receptor (V2R) and the V2R W164S mutant (that causes nephrogenic diabetes insipidus) have different post-endocytic targeting. The sorting of endocytosed myc-tagged WT and W164S V2R was determined by indirect immunolabeling of internalized receptors in transiently transfected COS7 cells. The WT and temperature (26 degrees C) rescued mutant receptors were labelled with anti-myc Ab in live cells (1h) and then chased in Ab-free medium (1h, 37 degrees C) before indirect immunolabeling. To mark lysosomes, cells were labeled with 10 kD Texas red–dextran at 50 µg/ml by overnight fluid-phase endocytosis and chased for &gt;3 h at 37°C. Fluorescence micrographs were obtained by a microscope (LSM510 or LSM710; Carl Zeiss, Inc.) equipped with a Plan-Apochromat 63×/NA 1.4 objective in multitrack mode. This single optical section shows that the WT V2R does not co-localize with lysosomes. A companion image shows that the internalized W164S V2R mutant, however, does co-localize with lysosomes.
description: Preparation: crosslinking-fixative fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: Alexa Fluor 488; TexasRed
Data qualification: Raw
DOI: 10.6075/j0028r8v
title: CIL: 53990. In Cell Image Library

description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
description: Visualization methods: confocal microscopy
description: STE family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
DOI: 10.6075/j0f18xqf
title: CIL:35131, Mus musculus, macrophage. 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: unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: Phase contrast microscopy of living bone marrow derived macrophages. These cells are highly motile and the snapshot catches lamella and ruffles where the cells are protruding and phase dense organelles inside the volumes of the cells.
description: Cells were extracted from a mouse femur and plated in a coverslip bottom well (MatTek) in standard culture media. The Olympus IX 71 microscope had a simple heated stage. Cells were imaged with a 60X N.A. 1.4 phase 3 planapo objective with a Cooke Sensicam QE operated by IP Lab software running on a Dell Windows XP computer.

This picture is one of a series that may be composed into a montage to see a large field of cells interacting while preserving the high magnification. Some of the pixels in this and the neighboring images are saturated.
DOI: 10.6075/j0fj2fgd
title: CIL:37404, Danio rerio, blastomere, yolk platelet. In Cell Image Library

description: A 2.75 hour Zebrafish embryo; the same embryo as in CIL 37403 --later in blastoderm development. The video shows dynamics in a perisagital section of the embryo. The sequence shows blastomeres dividing asynchronously. The surface cells begin to take on epithelial characteristics. A distinct yolk syncytial layer emerges. At each prophase, rapid movements of yolk platelets occur within the yolk. This video made available by Mark Cooper thru Zebrafish - The Living Laboratory. The videos in this group can also be found in the Developmental Landmarks page of the Fishscope web site.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
Data qualification: Raw
DOI: 10.6075/j0tq61ps
title: CIL:40003, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Transgenic mice (strain DATKO) from Duke University were perfused with aldehyde fixatives (4% paraformaldehyde + 0.1% gluteraldehyde), sectioned on Vibratome (thickness, 80 µm), and rinsed in phosphate buffered saline (PBS,3 x 10min) and incubated in blocking buffer (PBS, 3% normal donkey serum, 1% fish skin gelatin, 0.3% Triton X-100, 1% bovine serum albumin). Tissue sections incubated on shaker overnight, 4° C in primary antibodies diluted in blocking buffer as follows: anti-VMAT-2; Host = guinea pig; 1:500 (Oncogene, catalog # 503-01-50);
anti-DARPP-32; Host = mouse; 1:500 (BD Transduction Laboratories, catalog #611520). Following 3 x 10' rinses, tissue was incubated for 2hr, RT, on a shaker in secondary antibodies diluted at 1:100 in working buffer (donkey-anti-mouse AF488 [Molecular Probes, Cat #A21202] and donkey-anti-guinea pig RRX [Jackson Immunoresearch Laboratories, Inc]. Following rinses in PBS, sections were mounted on slides with gelvatol. Individual images were gathered using a BioRad RTS 2000 Multiphoton with a Nikon PlanApo objective (N.A. 1.45).
description: Preparation: formaldehyde fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody; Alexa Fluor 488; X-Rhodamine
Data qualification: Processed
description: Large scale brain mosaic showing the distribution of the dopamine receptor-associated phosphoprotein DARRP-32 (green) and the vesicular monamine transporter VMAT-2 (red) in a hemisection through the anterior neostriatum of a dopamine transporter knock out mouse. This image was generated by tiling 45 by 65 (X, Y axes) frames of maximum projection images in the Z-axis. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
DOI: 10.6075/j0r78d88
title: CIL:2759, Caenorhabditis elegans. In Cell Image Library

description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 8 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
DOI: 10.6075/j0668d62
title: CIL:10115, Rattus, multipolar neuron. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; differences in adsorption or binding of stain
Visualization methods: phalloidin; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
description: This multi-layer image shows the spatial relationship between filamentous actin (red) and microtubule array (green) in cultured hippocampal neurons, grown for 5 days in vitro. Actin staining (with rhodamine phalloidin) highlights the growing tips and filopodial extensions along axons and dendrites, while microtubule staining reveals the stable shafts of these processes. Some nonneuronal cells may also appear in the field.
Detailed Methods: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4, 37°C, 15 minutes), permeabilized (0.25% Triton, 7 minutes) and immunostained for tubulin (monoclonal DM1A, Sigma, with Alexa 488 conjugated secondary, Molecular Probes, excitation, 494, emission, 519) and rhodamine-conjugated phalloidin (Molecular Probes, excitation, 540, emission, 565). Fluorescent and phase images were acquired with a Leica DMRA microscope with a mercury arc lamp, a 20X lens (HC PL Fluotar, NA 0.5), Leica GFP filter set (excitation, BP 470/40; dichromatic mirror, 500, suppression filter, BP 525/50); Leica N3 filter set (excitation, BP546/12; dichromatic mirror, 565, suppression filter, BP 600/40), Photometrics CoolSnap ES CCD camera and MetaMorph software.
DOI: 10.6075/j0k35stx
title: CIL:12103, Colpoda cucullus, 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; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; Print from negative scanned to Photoshop.
Data qualification: Processed;spatialmeasurements
description: A layer of mucocysts is docked under the pellicle. The pellicle has a plasma membrane and an alveolar sac system. Both basal bodies of a dikinetid are ciliated, and the food vacuoles are plentiful and filled with bacteria. TEM taken on 6/5/69 by R. Allen with Philips 300 operating at 60kV. Neg. 4,270X. Bar = 1µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. A high resolution image is available in the library (CIL:38866) and can be used in quantitative analysis. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections were prepared at approximately 75nm thickness. Additional information is available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0pz57zn
title: CIL:9198, Homo sapiens, permanent cell line cell, epithelial cell. In Cell Image Library

description: Sialyl Transferase-EGFP transfected HeLa cells demonstrating the redistribution of the Golgi Apparatus to the Endoplasmic Reticulum upon treatment with Brefeldin A (BFA). 
Images were collected as a 4D time series (z-stack over time). z-stacks of 48 individual timepoints are included in this collection of files as well as the movie SiEGFP_BFA.avi, which is the maximum projection of the z-stacks at the individual time points.

BFA was added according to the following protocol:
Timepoint1: Before addition of BFA 0seconds (8 Z-slices at 1 um apart)
Timepoint2: After addition of BFA 130seconds (8 Z-slices at 1 um apart) 
Timepoint3: 238 seconds (11 Z-slices at 1 um apart) 
Timepoint3 thru Timepoint48: Images captured every 5 seconds (11 Z-slices at 1 um apart at each time point) 

Images were collected on a Carl Zeiss spinning disk confocal with a 63X 1.4 NA objective with 250 ms exposures at 5 s intervals.
description: Preparation: unfixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: unprocessed raw data
DOI: 10.6075/j0hx1bcv
title: CIL:13465, Saccharomyces cerevisiae S288c. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: constrained iterative deconvolution
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
description: Kre2-GFP is not efficiently maintained in the Golgi apparatus when Pik1-mediated PtdIns4P synthesis ceases, implicating Pik1 signaling in retrograde trafficking of Golgi residents. In this image, Kre2-GFP is expressed in the pik1-83 mutant strain after shift to restrictive temperature of 37C for 1h. Cells grown in liquid medium were mounted in growth medium and 3D image stacks were collected at 0.4-µm z increments on a DeltaVision workstation (Applied Precision) based on an inverted microscope (IX-70; Olympus) using a 100× NA 1.4 oil immersion lens. Images were captured at 23C with a 12-bit CCD camera (CoolSnap HQ; Photometrics) and deconvolved using the iterative-constrained algorithm (Agard, 1984) and the measured point spread function. One image from the approximate center of z stack is shown in Fig4D 37C pik1-83 panel in J Cell Biol. 187: 967-975. 2009. Images in Fig 4D include CIL#s 13460, 13461, 13462, 13463, 13464, 13465, 13466, 13467.
DOI: 10.6075/j0mp52fg
title: CIL:12921, 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, as indicated by peripheral labeling with adipophilin (smaller gold particles) and elements of the trans-Golgi network, identified by TGN38 (a transmembrane trans-Golgi protein) staining (larger gold particles). Note that trans‐Golgi 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: 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 adipophilin (guinea pig anti-adipophilin) and TGN38 (mouse monoclonal 2F7) and colloidal gold-conjugated secondary antibodies (15 nm anti-mouse, 10 nm anti-guinea pig; 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 21,000 X. See Ladinsky and Howell (2007) for more information on methods used.
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
DOI: 10.6075/j03f4n7c
title: CIL:27842. In Cell Image Library

description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
description: One of the principal challenges in counting or segmenting nuclei is dealing with clustered nuclei. To help assess algorithms' performance in this regard, this synthetic image set consists of five subsets with increasing degree of clustering. Five subsets of 20 images each are provided. Each image contains 300 objects, but the objects overlap and cluster with overlap probability ranging from 0.0 to 0.6, and can be found with CIL 27833, 27853, 28754, 28734, and 28714, respectively. This image set has 0.0 probability overlap. The images were generated with the SIMCEP (http://www.cs.tut.fi/sgn/csb/simcep/tool.html) simulating platform for fluorescent cell population images (Lehmussola et al., IEEE T. Med. Imaging, 2007 and Lehmussola et al., P. IEEE, 2008). Ground truth for foreground/background segmentation are available as binary images as the second image in the tiff image stack. 
Recommended citation "We used the Synthetic 1 image set (Ruusuvuori et al., in Proc. of the 16th European Signal Processing Conference (EUSIPCO-2008), 2008), available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
DOI: 10.6075/j0z60n59
title: CIL:2804, Caenorhabditis elegans. In Cell Image Library

description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 8 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
DOI: 10.6075/j0rn3719
title: CIL:2258, Caenorhabditis elegans. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 6 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.