cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0sn07v7
title: CIL:41689, Homo sapiens, osteocarcinoma. In Cell Image Library

description: Preparation: chemically fixed tissue; permeabilized tissue
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 epitope
Visualization methods: primary antibody plus labeled secondary antibody
description: Single slice confocal images representing one optical slice of a cell stained for the Human Protein Atlas (HPA) antibody 
 HPA027999 (shown in green). HPA027999 is a polyclonal anti-ATPIF1 antibody that labels mitochondria. The cells are also stained with reference markers in order to facilitate the annotation of the subcellular distribution of the protein targeted by the HPA antibody. The following probes/organelles are used as references; (i) DAPI for the nucleus (blue) and (ii) anti-tubulin antibody as internal control and marker of microtubules (red).
description: The use of data and images from this site in publications and presentations is permitted provided that the following conditions are met: The publication and/or presentation are solely for informational and non-commercial purposes. The source of the data and/or image is referred to this site (www.proteinatlas.org) and/or the above publication is cited.
DOI: 10.6075/j0ng4png
title: CIL:8471, 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
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: Development of axon and dendritic arbors in cultured hippocampal neurons after 2 days in vitro. At this timepoint, many, but not all cells are polarized, evidenced by the absence of a long, slender axon. MAP2 staining (red) is becoming segregated to the dendrites, while microtubule staining (green) reveals both the axons and dendrites in the field of view. Nonneuronal cells (e.g. glia) are infrequent, but may also be present in this preparation. 

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), permeabilized with 0.25% Triton and immunostained for tubulin (monoclonal DM1A, from Sigma with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and MAP2 (polyclonal Ab266, from S. Halpain with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 40X (HCX PL APO, NA 1.25) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. This merged image was generated with the MetaMorph color combine function.
DOI: 10.6075/j0qc02jr
title: CIL:9159, 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/j07d2t0f
title: CIL:26546, Mus musculus, fibroblast. In Cell Image Library

description: Cells were cultured in DME (Invitrogen) supplemented with 10% fetal bovine serum and 100 U/ml penicillin/streptomycin (Invitrogen) at 37°C in a humidified 5% CO2 incubator. Scrambled siRNA transfected NIH3T3 cells were treated with DMSO for 30 min, and co-stained for betaPIX (green) and actin (red, phalloidin). Images were captured by Olympus IX81-ZDC inverted microscope with UPlanFL N 40X objective.
description: To study the molecular mechanism by which nonmuscle myosin II (MII) regulates protrusion and adhesion dynamics in migrating cells, NIH3T3 cells were treated with scrambled siRNA (Scr) for 2 days, treated with blebbistatin (BBS) for 30 min., and stained for βPIX (green) and actin (red). These findings help elucidate a functional link between MII and Rac1/Cdc42 GTPases, which may regulate protrusion/adhesion dynamics in migrating cells. This image is the original data file from Fig. 6B, “Requirement for βPIX in MII-regulated cell protrusion and adhesion.” J. Cell Biol. 2010. Vol. 190(4):663–674.
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
Visualization methods: Alexa Fluor 488; Tetramethyl rhodamine (TRITC); phalloidin
Data qualification: Raw
DOI: 10.6075/j0hq3z93
title: CIL: 50693, FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles. In Cell Image Library

description: FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles. Postnatal day 4 mouse Inner Ear Organ of Corti labeled with anti-PKHD1L1 antibody (10 nm gold beads). The dataset represents the apical end of the Outer Hair Cell with the stereocilium bundle. Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample.
description: Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample. 
2.6_Cell_2_GoldParticle_Segmentation is a multipage TIFF file illustrating the gold bead segmentation results (1.95×1.95×10 nm³ voxel size). Same as ‘GoldParticles.am’ file used for MATLAB volume analysis of this cell, but converted to TIFF to allow for its online preview.
This file is a part of Dataset 2, comprised of files related to the Cell #2 of current study. The numbering order of the files reflects the order of operations performed during the analysis.
description: Imaging mode: Serial electron microscopy; focused ion beam scanning electron mictoscopy (FIB-SEM)
Visualization methods: Heavy metal stain (osmium tetroxide, potassium ferrocyanide, tannic acid), immunogold labeling using 10 nm gold beads
DOI: 10.6075/j06t0kw8
title: CIL:248, Mus musculus, fibroblast. In Cell Image Library

description: Preparation: methanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: microscopy
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: localized accumulation of fluorescent probe
Visualization methods: Alexa Fluor 594; Alexa Fluor 488; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
description: The distribution of mitochondria (labeled with antibody to heat shock protein 70) in relation to intermediate filaments (labeled with vimentin antibody) 16 hours after release from serum starvation in methanol-fixed 3T3 fibroblasts.

Microscope - Zeiss Axioplan I
Illumination - Mercury arc lamp
Objective - 100X oil/1.3 NA
Intermediate lens between obj and camera - 0.63X
Camera - Axiocam MRM CCD
Filters: 
1. Ex 485/20, Em 515-565 BP, dichroic 510
2. Ex 560/40, Em 630/60, dichroic 595
DOI: 10.15468/dl.atu7ye
title: Occurrence Download

description: A dataset containing 55109 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is one of (Asia, Europe)",
 "Month is one of (April, May, June, July, August, September, October)",
 "TaxonKey is Anas clypeata"
 ]
}

 The dataset includes 55109 records from 545 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009695-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0wq03cx
title: CIL: 52853, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: One z layer of a z-stack at the given tile position
description: Tile x=4, y=4, z=9 from PS11_167511L_Myc_Terc
DOI: 10.6075/j0tb16f1
title: CIL: 52576. In Cell Image Library

description: One z layer of a z-stack at the given tile position
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: Tile x=1, y=6, z=5 from PS09_20676_2B_Myc_Terc
DOI: 10.6075/j0dr2t47
title: CIL:12578, Spiroplasma kunkelii, Zea mays, plant cell, prokaryotic cell. In Cell Image Library

description: Preparation: tissue in epoxy resin embedment; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: osmium tetroxide; lead salt; uranyl salt
Data qualification: Processed
description: Detailed methods: Tissue was processed for TEM by fixation in glutaraldehyde and osmium tetroxide, embedded in Spurr's medium. Thin sections were stained with uranyl acetate and lead citrate, and examined by a Philips-201 TEM (non-digital camera). Negatives were scanned later to generate these electronic files.
description: Electron micrograph of corn stunt spiroplasma (CSS, Spiroplasma kunkelii, Class Mollicutes) in sieve elements and other phloem cells of infected maize leaves. CIL:19116, from the same image group, is a labeled version of this image. CSS is a wall-less procaryote that causes corn stunt disease and is biologically transmitted by some leafhopper species, e.g. Dalbulus maidis and D. gelbus (Hemiptera, Cicadellidae). Spiroplasma cells are limited by a unit membrane with no cell wall. They can be quasi-spherical, pleiomorphic or maintain a filamentous/spiral form. CSS multiplies in both plant and insect hosts and is transmitted with salivary secretions during feeding of the vector on new host plants. Additional images are available by this contributor.
DOI: 10.6075/j0df6px9
title: CIL:13908, Homo sapiens, permanent cell line cell. In Cell Image Library

description: Human colon carcinoma HCT 116 cells were transfected with an siRNA specific for SIRT1 and then retransfected with a GFP-LC3-encoding plasmid, cultured in complete medium for 24 h and treated with 100 µM sperimidine for 4 h. For fluorescence microscopy determinations, cells cultured on coverslips were fixed in paraformaldehyde (4% wt/vol) for 15 min at RT, washed three times in PBS, and mounted with mounting medium (Vectashield). Confocal fluorescent images were captured using a confocal fluorescence microscope (TCS SP2; Leica) fitted with an Apochromat 63× 1.3 NA immersion objective. Images were acquired with a camera (DFC 350 FX 1.8.0; Leica) using LAS AF software (Leica) and processed with Photoshop (CS2; Adobe) software. Specifically, picture processing involved cropping of representative areas and linear adjustments of contrast and brightness and was performed using Photoshop (with equal adjustment parameters for all pictures); no explicit γ correction was used. Image: Figure 1A, bottom right panel, in Morselli et al. J Cell Biol 192: 615-629
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue; cultured cells in vitro
Item type: recorded image; charge coupled device (CCD)
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: brightness and contrast adjusted
Data qualification: Processed;intensitiesquantitation
DOI: 10.6075/j0k35t0k
title: CIL:37382, damselfly, flight muscle cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; lead salt
Processing history: digitized negative film
Data qualification: Raw;spatialmeasurements
description: Longitudinal and cross sections showing ribbon like myofibrils regularly alternating with layers of mitochondria and SR/T tubules. Dyads are located in a grove of the mitochondrial surface. Negatives aere scanned on nikon 8000 at 4000dpi/6.3 micron scan step size, then reduced in size 4X for upload, for an effective pixel size of 25 micron.
 
 Technical details:
 Heads and tail removed, thorax bisected and immersed in 3% glutaraldehyde buffered in 0.1 M cacodylate buffer (pH7.2). Stored at 4C for several days. Muscle dissected out. Rinsed 3Xin buffer, postfixed in 2% PsO4 in buffer, for 1.5 hrs; rinsed 3 times in water, en-block stained in saturated aqueous uranyl acetate, embedded in Spurr. Thin sections stained in uranyl acetate and lead and examined in a Philips 410 Microscope.
 
 Reference for the image:
Loesser, K.E., Castellani, L. and Franzini-Armstrong, C. Disposition of junctional feet in muscles of invertebrates. J. Muscle Research Cell Motility 13:161-173, 199
DOI: 10.6075/j0qr4ws4
title: CIL: 53566, Homo sapiens, HeLa. 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: AGC 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/j0tb15xw
title: CIL:2684, 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: 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: 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/j0p849sz
title: CIL:27222, Homo sapiens, blood cell, red blood cell. In Cell Image Library

description: Preparation: dispersed cells
Relation to intact cell: whole mounted cells
Item type: recorded image; threshold image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: differences in intrinsic optical density
Visualization methods: visualization of contiguous regions
Processing history: threshold
description: This image set consists of five differential interference contrast (DIC) images of red bood cells (approximately 8 microns in diameter). Each image in the set contains a DIC image and a thresholded image. There are two options when using this data set to quantify an algorithm's effectiveness. The simplest method is simply to compute the percentage of pixels that your algorithm and the thresholded image have in common. However, a wide class of algorithms for handling DIC images do not explicity segment the image, but rather transform the image so that it can later be thresholded. These images were obtained from http://www.broadinstitute.org/bbbc/human_rbc_dic.html

DIC images attributed to Skerker, Rush, and Wiegand; the thresholded images attributed to Morgan.
DOI: 10.6075/j0kp80z6
title: CIL:24784, Xenopus laevis, fibroblast. In Cell Image Library

description: Localization of XAC (Xenopus ADF/cofilin) in Xenopus fibroblasts. Immuno-EM with XAC antibody at low magnification. High magnification view is available at CIL 24785. Nucleus and surrounding regions look bright because of high content of cellular proteins, which creates high electron density (brightness in inverted contrast). Immunogold-labeling in these central regions is very low. Image corresponds to Figure 10h from J Cell Biol. 1999 May 31;145(5):1009-26.
description: Preparation: permeabilized tissue; glutaraldehyde fixed tissue; polyethylene glycol
Relation to intact cell: dispersed cell in vitro
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: optical path length gradient
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating; primary antibody plus labeled secondary antibody; platinum replica; immuno gold
Processing history: unprocessed raw data
description: Procedures for detergent extraction, immunostaining, S1 decoration, light, and EM were described previously (Svitkina et al., 1995, 1996, 1997;Verkhovsky et al., 1995; Svitkina and Borisy, 1998).
DOI: 10.6075/j0ks6qw8
title: CIL:39576, Saccharomyces cerevisiae. In Cell Image Library

description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Cdc15, a protein kinase involves in cytokinesis. These phase and GFP z-series images are part of an image group containing CIL 39576-39580. Note that there are additional groups of images of other cell cycle regulator proteins by the same authors available 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; elastic scattering of photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
Data qualification: Raw;spatialmeasurements
description: The images were acquired using a 60x 1.42 NA objective lens on Delta Vision system equipped with CoolSNAP_HQ2 / HQ2-ICX285. Please read the microscopy section of the referenced paper for details before image analysis.
DOI: 10.6075/j03j3c9m
title: CIL:40382, Solenostemon scutellarioides, epidermal cell. In Cell Image Library

description: Image collected on a Zeiss DSM 962 SEM. Complete specimen preparation protocol available at:
http://remf.dartmouth.edu:8080/EM-Wiki/36
description: Preparation: glutaraldehyde fixed tissue; critical_point dried specimen; ethanol dehydration
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide; shadowing and plating
Processing history: unprocessed raw data
description: Scanning electron microscope image of cross-section through a Solenostemon scutellarioidesi (coleus) stem. The image shows trichomes (hair-like projections) on the surface of the epidermis.This image is part of a group on botanical stems (CIL:40378-40395).