cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j09k497g
title: CIL:7108, Homo sapiens, neuron. In Cell Image Library

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 molecules appear as bright particles in AFM images. Volume measurements of the complexes suggest that MeCP2 monomers (circular particles) and dimers (larger elliptical particles) are present and suggest that MeCP2 binds DNA cooperatively. Other images in the grouped 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 and relevant to the in vivo interactions between MeCP2 and chromatin.
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: unprocessed raw data
DOI: 10.6075/j07d2tmh
title: CIL: 51971, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: A novel cell population analysis to quantify both initial and long-term drug effects, namely pseudopod adaptation and recovery following an initial drug-induced perturbation, adding drug slowly in 1/4 increments over 90 minutes.
description: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

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.
description: Imaging mode: DICM
Visualization methods: Spinning disc confocal DICM & widefield DICM Using a Nikon TiE microscope equipped with a 40x, 0.95 N.A. objective and a Hamamatsu ORCA-Flash 4.0 V3 Digital CMOS camera, or a Nikon TiE spinning-disc confocal microscope equipped with a Yokogawa CSU-X1 scanning unit, an Andor iXon 888 EMCCD camera, and a 60x, 1.3 N.A. water-immersion objective or a 40x, 0.95 N.A. objective
DOI: 10.6075/j0wd3zr7
title: CIL:1074, Caenorhabditis elegans, muscle cell. In Cell Image Library

description: C. elegans muscle age is a data set of fluorescence 20X microscopy images of C. elegans nematodes stained with phalloidin to visualize actin in muscles at different ages (1,2,4, and 8). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1005, 1057, 1105, and 1265, respectively.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: phalloidin
Processing history: unprocessed raw data
description: The purpose of the dataset C. elegans muscle aging is to deduce the age of the nemathode based on images of muscles. Images of C. elegans were taken at different chronological ages. This image is part of the day 2 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.
DOI: 10.6075/j0nc60vm
title: CIL: 53270, Homo sapiens, Lung adenocarcinoma cells. In Cell Image Library

description: Nucleolar expression of PAX8 in lung adenocarcinoma cells
description: Imaging mode: recorded image
Visualization methods: Microscope photography
description: Immunohistochemistry
DOI: 10.6075/j09g5mxh
title: CIL:39615, Saccharomyces cerevisiae. 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
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.
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.
DOI: 10.6075/j08w3bzq
title: CIL:38704, Chlamydomonas reinhardtii. In Cell Image Library

description: Preparation: cryofixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Data qualification: Processed
description: Isolated chloroplast membranes of the unicellular photosynthetic alga Chlamydomonas reinhardtii were cryofixed, freeze-fractured, and surface replicas observed by transmission electron microscopy. These thylakoid membranes from this mixotropically grown ac-5 mutant show the particle size and distribution typical of unstacked membranes. See Fig 16 in Goodenough and Staehelin 1971 J Cell Biol 48:595-619.
description: Membranes were prepared, cryoprotected with glycerol, cryofixed, fractured at -100C, shadowed with Pt, and replicas prepared by carbon coating. Cleaned replicas were examined with a Philips 300 TEM. See Goodenough and Staehelin 1971 J Cell Biol 48:595-619.
DOI: 10.6075/j0fx79ks
title: CIL:42154, Mus musculus. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: mammary organoids
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: contrast adjustment
description: Representative time-lapse movie of a normal mouse mammary fragment in collagen I. Images collected every 20 minutes. This movie is part of a group of movies that include CIL 42151-42168.
DOI: 10.6075/j0nc5zw8
title: CIL:13678, Drosophila melanogaster, motor neuron. In Cell Image Library

description: The JNK phosphatase puckered, whose expression can be reported via a lacZ enhancer trap, is expressed in very low levels in uninjured neurons; however, nerve crush induces a dramatic increase in puc-lacZ expression in injured motoneurons. This image stack shows puc-lacZ (green) and neuronal nuclei (red) in a third instar larva injured at site 1 (as defined in Fig 1C). Wandering third instar larvae were dissected in PBS and fixed in either 4% paraformaldehyde in PBS or Bouin's fixative for 15–30 min. Primary antibodies used were: rat anti-elaV (7E8A10, Developmental Studies Hybridoma Bank) and mouse anti-lacZ (40-1a, DSHB). Secondary antibodies were Alexa 488 anti-mouse and Cy3 anti-rat. Confocal images were collected at room temperature on a spinning-disk confocal system (PerkinElmer) consisting of a scanner (Nipkow CSU10; Yokogawa) and an electron microscopy charge-coupled device camera (C9100-50; Hamamatsu Photonics) mounted on an inverted microscope (Axio Observer; Carl Zeiss, Inc.) with 25× 0.8 NA multi and 40× 1.3 NA, 63× 1.5 NA, and 100× 1.46 NA oil objectives. Similar settings were used to collect all compared genotypes. All imaging and quantification were conducted with Volocity software (PerkinElmer). This image stack corresponds to Fig 1E1 in J Cell Biol. 2010. 191: 211-223. Images in Fig 1 include CIL#s 13676, 13677, 13678, 13679.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: primary antibody plus labeled secondary antibody; beta-galactosidase; Alexa Fluor 488; Cy3
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0gf0tgg
title: CIL:35423, Mus musculus, oocyte. In Cell Image Library

description: Time-lapse microscopy of a b-Tubulin GFP expressing mouse oocyte injected with siCo-5h, a control siRNA. Images were taken every 20 minutes. Times after the resumption of meiotic maturation and germinal vesicle breakdown (GVBD) are indicated in the lower left corner.
 Video S3. Found at: doi:10.1371/journal.pone.0003338.s003
description: Time-lapse images were acquired using a Photometrics CCD camera (CoolSnap HQ2) mounted on a Leica DMI600B microscope using a Leica HC PL APO 20X/0.7 NA objective enclosed in a thermostatic chamber (Life Imaging Services). Immunofluorescence methods can be found in the cited paper and in Brunet S. et al. (1999) J Cell Biol 146: 1–11.
description: Preparation: living 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 a specific protein
Visualization methods: Green fluorescent proteins from Aequorea; visualization of contiguous regions
Processing history: unprocessed raw data
Data qualification: Raw
DOI: 10.6075/j0m32tz9
title: CIL:1080, Caenorhabditis elegans, muscle cell. In Cell Image Library

description: The purpose of the dataset C. elegans muscle aging is to deduce the age of the nemathode based on images of muscles. Images of C. elegans were taken at different chronological ages. This image is part of the day 2 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: C. elegans muscle age is a data set of fluorescence 20X microscopy images of C. elegans nematodes stained with phalloidin to visualize actin in muscles at different ages (1,2,4, and 8). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1005, 1057, 1105, and 1265, respectively.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: phalloidin
Processing history: unprocessed raw data
DOI: 10.6075/j0d79b21
title: CIL: 53393, Plankton. In Cell Image Library

description: Diatom
description: Imaging mode: Holography
Visualization methods: Amplitude Mode
description: 128x128 segmented image from volumetric hologram
DOI: 10.6075/j05d8rzt
title: CIL:39560, 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; visualization of contiguous regions
Processing history: unprocessed raw data
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Clb2. Clb 2 is a cyclin-dependent protein kinase regulator, involving in G2/M transition of mitotic cell cycle and positively regulating spindle pole body separation. These phase and GFP z-series images are part of an image group containing CIL 39556-39560. Note that there are additional groups of images of other cell cycle regulator proteins by the same authors available in the Library.
description: Time-lapse images were collected on a DeltaVision system (Olympus IX71) with 60x/1.42 NA objective at 5 minute intervals. Please read the microscopy section of the referenced paper for details before image analysis.
DOI: 10.6075/j0610zqn
title: CIL: 50990, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: populations of ~1200 cells plated on glass in standard media were imaged at 37º C in each experiment. A target subpopulation of ~100 cells display a readily observed extended, ruffling leading edge pseudopod . The cells exhibiting these deployed, extended pseudopods were counted in each unit area at 6 timepoints during the 3 hr observation period following rapid addition of drug to its standard working concentration. Altogether, 6 experiments were carried out for each treatment, yielding average timecourses summarizing observations of ~600 polarized cells.

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.
description: A novel cell population analysis to quantify both initial and long-term drug effects, namely pseudopod adaptation and recovery following an initial drug-induced perturbation, adding a full therapeutic dose at once at t=0.
description: Imaging mode: DICM
Visualization methods: Spinning disc confocal DICM & widefield DICM Using a Nikon TiE microscope equipped with a 40x, 0.95 N.A. objective and a Hamamatsu ORCA-Flash 4.0 V3 Digital CMOS camera, or a Nikon TiE spinning-disc confocal microscope equipped with a Yokogawa CSU-X1 scanning unit, an Andor iXon 888 EMCCD camera, and a 60x, 1.3 N.A. water-immersion objective or a 40x, 0.95 N.A. objective
DOI: 10.6075/j0086404
title: CIL:37250, Chlamydomonas. In Cell Image Library

description: An electron micrograph of a potion of a cell of the unicellular alga Chlamydomonas reinhardii illustrating the eye spot, an organelle found inside the chloroplast that is composed of red carotenoid pigments and photoreceptive proteins and functions in phototaxis. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
description: Preparation: chemically fixed tissue; tissue in plastic embedment
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide
Processing history: unprocessed raw data
description: Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original magnification 43,000.
DOI: 10.6075/j09z942v
title: CIL:10546, 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: Yellow fluorescent proteins from Aequorea; mCherryFP
Processing history: 3D-deconvolution
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
description: A monolayer of human foreskin fibroblast cells was infected with Toxoplasma gondii expressing YFP-tagged TgIMC1 (innermembrane complex scaffold protein) and mCherry-tagged human alpha1tubulin. Images acquired using API DeltaVision on a Olympus IX70 inverted microscope. Objective: Olympus 60X water immersion, 1.2 NA. Filters: mCherry, ex 555-592 em 600-665, YFP, ex 490-510 em 525-595. Captured with CoolSnapHQ/ICX285. Image stack corresponds to raw data stack: CIL# 10545, maximum projection stack: CIL# 10547 and raw data stack with DIC: CIL# 10542. 

Unpublished image that is similar to images published in PMID: 16518471. See publication for other experimental details.
DOI: 10.6075/j0833r06
title: CIL:35210, Mus musculus, fibroblast. In Cell Image Library

description: Time lapse movie of mouse embryonic fibroblasts in culture imaged at 30 second intervals by phase contrast microscopy. A micropipette is positioned near the cells to deliver either a growth factor or control buffer. In this sequence a PDGF-AA is added and cells extend rapidly and turn to the pipette tip.
description: These data were collected as research which led to the published article Cell Physiol Biochem 2010;25:279-292.

Microscopy was performed with a 20X planapo phase contrast objective on an Olympus IX 70 microscope with a SensicamHQ cooled CCD camera and a heated stage insert set to 37 degrees C. Cells were grown and serum starved for 48 h in a coverslip bottom MatTek dish. Small amounts of PDGF-AA were continuously ejected from the micropipette to create a gradient in the vicinity of growth-arrested wt MEFs. Cell movement was monitored with time lapse video microscopy, taking images at 30 second intervals. A Femtojet Micromanipulator 5171 (Eppendorf-Brinkman Instruments) and a pump (model Femtojet; Eppendorf) were used to control the position of the micropipette and the pressure required for the chemoattractant flow. Femptotip II micropipettes were positioned within 1 μm of the cover slip and pressure set at 30 to 45 hPa. Spatial scale is approximate.
Imaging performed at the Image Analysis Facility of the Albert Einstein College of Medicine.
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
DOI: 10.6075/j0gf0t40
title: CIL: 53072, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given image
description: Image 4, z=18 from SC_028
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
DOI: 10.6075/j00c4ttf
title: CIL:7343, Opercularia [NCBITaxon:168247], Opercularia coarctata, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: A high resolution view of the contractile, sub-cortical myonemal sheet of Opercularia coarctata. Decorated ER tubules are intimately associated with the myonemal sheet. And pellicular pores or clathrin coated pits are evident in this grazing section through the periphery of the cortex. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol, and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. TEM taken on 6/13/69 by R. Allen with Philips 300 operatinjg at 60kV. Neg. 14,800X. The raw film was scanned with an Epson Perfection V750 Pro. This high resolution image is available for quantitative analysis.

Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; 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; unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation