cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j070805w
title: CIL:13889, Saccharomyces cerevisiae. In Cell Image Library

description: Cells (MATa nud1::kanMX4 leu2::nud1-2::LEU2 pRS316::eGFP-CNM67–TEM1) grown at restrictive temperature 37C were fixed in 2.5% formaldehyde for 10 min, washed twice, and resuspended in 0.1 M potassium phosphate buffer, pH 6.4. Cells were then fixed for 10 min in 80% ethanol and resuspended in 1 mg/ml DAPI. Imaging was performed at 25C using a Leica DM6000 microscope equipped with a 100x/1.40 NA oil immersion objective lens, A4, L5, and TX2 filters, and a digital CCD camera (DFC350, Leica). Pictures were processed with LAS AF (Leica) and ImageJ software.
description: Preparation: formaldehyde fixed tissue; ethanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: widefield illumination; fluorescence microscopy; differential interference contrast microscopy
Parameter imaged: fluorescence emission; optical path length gradient
Source of contrast: distribution of a specific protein; boundaries between regions with different refractive index; compartmentalization of stain or label
Visualization methods: EGFP; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Tem1 (green) constitutively targeted to spindle pole bodies in nud1-2 cells at the restrictive temperature still displayed problems positioning the spindle (this image shows a misaligned spindle, CIL #13873 shows an aligned spindle and CIL# 13874 shows a rebudded cell) typical of nud1-2, despite the fact that viability was restored. Nud1 is required for mitotic exit and constitutive targeting of Tem1 recovered the mitotic exit defect of nud1-2 cells. DAPI (blue) and differential interference contrast (DIC) image are also shown. Image is Fig 7F, middle panels, in J Cell Biol. (2011) 192: 599-614. Images in Fig 7 include CIL #13888, 13872, 13813, 13889, 13874.
DOI: 10.6075/j00c4tq3
title: CIL:36484, Xenopus laevis, fertilized egg. In Cell Image Library

description: This image is part of a large data set of Xenopus laevis eggs imaged at various times post fertilization (the first number of the file name corresponds minutes, eg 30_2 is 30 min post fertilization). The embryos are stained for alpha-tubulin (green) using a directly labeled B-5-1-2 antibody and DNA (red).
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: distribution of epitope; distribution of a specific protein
Visualization methods: labeled primary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Images collected on a Zeiss LSM 710 confocal with a 10X 0.3 NA objective using 561 and 633 laser lines.
DOI: 10.6075/j0bk1cf5
title: CIL:39663, Saccharomyces cerevisiae. In Cell Image Library

description: Images were collected at 4-minute intervals on a DeltaVision system equipped with a with a 60x PlanApo
PH3 phase-contrast, oil immersion objective (NA = 1.4). This system has a motorized x-y-z stage, automatic focusing, motorized illumination shutters and a CoolSNAP_HQ2 camera.
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
description: 10-hour timelapse of Wild-type Saccharomyces cerevisiae growing in 2% raffinose. These experiments are the control experiments used for comparison to the effects of the double mutant Clb2dbŒî, Clb5Œî on the cell cycle control system in budding yeast. The images from two experiments done with Wild-type Saccharomyces cerevisiae are available as CIL:39606-39625 and CIL:39646-39665. The images from two experiments done with the double mutant Clb2dbŒî, Clb5Œî are available as CIL:39626-39645 and CIL:39666-39685.
DOI: 10.6075/j0mg7n3q
title: CIL:47678, Staphylococcus aureus, neutrophil, endothelial cell. In Cell Image Library

description: Visualization of neutrophil recruitment in capillaries proximal to agarose beads. (Figure 1)
description: Relation to intact cell: intact cells-in vivo imaging
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Source of contrast: antibody labelling
Processing history: Converted from volocity to .avi
description: Mice were anesthetized with ketamine/xylazine, and then subcutaneous tissue on a dorsal flap was exteriorized. GFP staphylococcus aureus beads were inserted. Antibodies were injected into the vasculature to label neutrophils (red) and endothelial cells (blue). Blocking antibodies against the molecule Mac1 were administered after 2 hours of infection.
DOI: 10.6075/j0571b6m
title: CIL:21739, Drosophila melanogaster, epithelial. In Cell Image Library

description: 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 DNA
Visualization methods: Hoechst 33342
Processing history: unprocessed raw data
description: Five different samples of Drosophila melanogaster Kc167 cells were stained with Hoechst 33342, a DNA stain. The last sample (labeled nodsRNA, CIL 21789) is of wild-type cells. Each of the other four samples (labeled 48, 340, Anillin, and mad2, CIL 21749, 21739, 21759, and 21773, respectively) has a different gene knocked down by RNAi. This is the set that were treated with 340 RNAi. There are 10 images of each sample, for a total of 50 images. The images were acquired on a Zeiss Axiovert 200M microscope. A recommended use for these five image sets is to algorithmically compute the number of cells in each image. A tab-delimited text file containing this information can be found at the URL indicated in the attribution box. The recommended citation when using these images is: "We used the Drosophila Kc167 1 image set (Carpenter, et al., Genome Biology, 2006) available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
DOI: 10.6075/j0v40t9j
title: CIL:10499, Toxoplasma gondii RH. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image; charge coupled device (CCD)
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP; mCherryFP
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: A monolayer of human foreskin fibroblast cells was infected with Toxoplasma gondii expressing EGFP-tagged TgCentrin2 and mCherry-tagged TgIMC1 (innermembrane complex scaffold protein). Images acquired using API DeltaVision on a Olympus IX70 inverted microscope. Objective: Olympus 100X oil immersion, 1.35 NA. Filters: EGFP, ex 450-490 em 500-540, mCherry, ex 555-592 em 600-665. Dichromatic mirror: Chroma 89021. Captured with CoolSnapHQ/ICX285. 3D stack image is raw data corresponding to deconvolved stack: CIL# 10500.
Unpublished image that is similar to images published in PMID: 16518471. See publication for other experimental details.
DOI: 10.6075/j0cf9p01
title: CIL:35543, Cricetulus griseus, ovary. In Cell Image Library

description: Preparation: coagulating-fixative fixed tissue
Relation to intact cell: isolated subcellular component
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
description: CHO cells were arrested in metaphase with colcemid, swollen in 75mM KCl, fixed, disrupted, and observed using High Voltage EM. This image was recorded with a specimen tilt angle of 54 degrees. Grouped with it is an image of the same area at a tilt angle of 46 degrees, providing an oblique stereo view of chromosome organization.
description: Metaphase-arrested cells were fixed with 3:1 ethanol:acetic acid, transferred to 50% acetic acid, and passed though a syringe to break cells. Drops of sample were placed on formvar coated grids, stained with uranly acetate, and critical point dried. Grids were observed with the Wisconsin HVEM at 1 MeV. See Ris (1981) Stereoscopic electron microscopy of chromosomes. Meth Cell Biol 22:77-96; Ris (1978) Preparation of chromatin and chromosomes for electron microscopy. Meth. Cell Biol 18:229-246.
DOI: 10.6075/j0gf0sjz
title: CIL:7425, Homo sapiens, neuron. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: microscopy; atomic force microscopy
Parameter imaged: specimen height
Source of contrast: specimen height
Processing history: Pixel value determine by specimen height
description: The protein MeCP2 binds to symmetrically methylated CpG dinucleotides and is thought to transmit the (generally) repressive signals encoded in DNA methylation patterns. Mutations in MeCP2 lead to Rett syndrome. Here, MeCP2-DNA complexes have been imaged by AFM (Digital Instruments Nanoscope) in air using human MeCP2 and an 828 bp DNA sequence containing several methylated CpGs. MeCP2, which appears as bright circles in AFM images, and volume measurements of the complexes suggest that MeCP2 monomers and dimers are present and that MeCP2 binds DNA cooperatively. Other images in the linked set show looped structures and large complexes containing multiple DNA strands and MeCP2 molecules. These configurations are likely promoted by the multiple independent DNA-binding domains of MeCP2.
DOI: 10.6075/j0c53kwd
title: CIL:35744, Saccharomyces cerevisiae. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission; elastic scattering of photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP
description: Time-lapse images were collected on a DeltaVision system (Olympus IX71) with 60x/1.42 NA objective at 5 minute intervals. Please see the microscopy section in the referenced manuscript for details for image analysis.
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP-tagged SIC1. 
 
 SIC1 is an inhibitor of Cdc28-Clb kinase complexes that controls G1/S phase transition, preventing premature S phase and ensuring genomic integrity; phosphorylation targets Sic1p for SCF(CDC4)-dependent turnover; functional homolog of mammalian Kip1
 
These phase,gfp images are part of an image group that ranges from CIL:35740-35759. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the Library.
DOI: 10.6075/j0bp028v
title: CIL: 52075, Homo sapiens. In Cell Image Library

description: A single molecule TIRFM assay was employed to measure the kinase activity of purified PI3K molecules on a supported lipid bilayer by counting the number of product PIP3 molecules they produce.
description: Imaging mode: Fluoresence
Visualization methods: objective based TIRFM using a modified Nikon TE-2000U (60x 1.49 N.A. TIRF objective) and illumination from a 532-nm solid-state laser with power modification by neutral-density filters
description: This assay utilizes physiological concentrations class I PI3Ka, 1mM ATP, drug identified in subfolder, and saturating concentrations of fluorescently-labeled GRP-PH domain, a PIP3 product lipid binder, in order to count each product lipid produced. Enzyme rates are calculated as the slope of product lipid created vs. time. 21.5 ± 0.5°C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
DOI: 10.6075/j0h130z4
title: CIL:36632, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; uranyl salt; lead salt; osmium tetroxide
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed
description: The tubular cristae of mitochondria bear a pair of protrusions when seen in cross section. These are the F1 subunits of F1F0 ATP synthase enzymes which play a role in producing ATP, the cell‚Äôs main energy source. TEM taken on 3/7/80 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 22,500X. Bar = 0.25µm.
DOI: 10.6075/j08s4nkv
title: CIL:34889, fibroblast. In Cell Image Library

description: Multiple branching of actin filaments in lamellipodia of vertebrate fibroblasts. This image shows a local enlargement of the leading edge shown in overview in CIL 24788. Image corresponds to Figure 1k from J Cell Biol. 1999 May 31;145(5):1009-26. Figures 1i-o correspond to CIL 24888-24893.
description: Preparation: permeabilized tissue; glutaraldehyde fixed tissue; phalloidin; polyethylene glycol
Relation to intact cell: dispersed cells 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; platinum replica
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/j0ks6qtc
title: CIL:1635, 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 0 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/j0dr2tk2
title: CIL:9182, 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/j0wq02sw
title: CIL:8781, Rattus, multipolar neuron. In Cell Image Library

description: This color combined image shows the spatial relationship between filamentous actin (red) and microtubule array (green) in cultured hippocampal neurons, grown for 1 day 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.
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). Images were acquired with a Leica DMRA microscope with a mercury arc lamp, a 40X lens (HCX PL Fluotar, NA 0.75), 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. Merged image was generated with the MetaMorph color combine function.
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
DOI: 10.6075/j0125r9g
title: CIL:34886, Xenopus laevis, keratocyte. In Cell Image Library

description: Preparation: permeabilized tissue; glutaraldehyde fixed tissue; phalloidin; polyethylene glycol
Relation to intact cell: dispersed cells 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; platinum replica
Processing history: unprocessed raw data
description: Multiple branching of actin filaments in lamellipodia of Xenopus keratocytes. This image show an enlargement of a local region from the overview of the leading edge, CIL 24786. Image corresponds to Figure 1f from J Cell Biol. 1999 May 31;145(5):1009-26. Figure 1b-1g are CIL 24882-24887.
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/j02r3qrb
title: CIL:18484, damselfly, flight muscle cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: unembedded tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: digitized negative film
Data qualification: Raw;spatialmeasurements
description: Most images show fractures through the outer membrane of mitochondria and SR/T tubules of dyads nestled in long grooves of the mitochondrial surface. All leaflets of the membranes appear in the images. This image is part of the group image CFA00512. TEM magnification 24400X. The negative film was scanned at LBL then reduced in size for upload. Scan step size is 6.3 micron, 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. pH 7.2. stored at 4C for several days. Muscle dissected out. Infiltrated in 30% glycerol in water. Frozen in liquid nitrogen cooled Freon, fractured in Balzers 400 Freeze-fracture, shadowed with platinum at 45o angle. Replicas were cleaned with Clorox (to remove tissue and with either sulfuric acid or NaOH to try removing the tracheolae. Replicas examined in a Philips 410 Microscope. Reference for these images: 
Takekura, H. and Franzini-Armstrong C. The structure of Ca2+ release units in arthropod body muscle indicates an indirect mechanism for excitation-contraction coupling. Biophys. J. 83, 83, 2742-2753, 2002.