cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j05d8qzd
title: CIL:13861, Prochloron. In Cell Image Library

description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: whole mounted tissue
Item type: film
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: Raw;spatialmeasurements
description: Freeze-fracture replica of the unicellular photosynthetic prokaryote Prochloron showing the distribution and size of particles on cleaved thylakoid membranes. 
This image group includes many other freeze-fracture images of Prochloron.

See also: Giddings TH, Withers NW, Staehelin LA.1980 Supramolecular structure of stacked and unstacked regions of the photosynthetic membranes of Prochloron sp., a prokaryote. Proc Natl Acad Sci U S A. 77:352-3566.
description: Prochloron was collected at Coconut Island, Oahu, Hawaii. Green colonies of didemnid ascidians, Diplosoma virens, were collected from shallow waters. Green spherical cells, identified as Prochloron, were released from the ascidians by gently pressing on the colonies while flushing the surface with sea water. Cells were centrifuged, then rinsed in filtered sea water fixed with glutaraldehyde, infiltrated with glycerol and vitrified. Samples were fractured and replicated using a Balzers BA 360 freeze-etch device and examined and in a JEOL 100C TEM at 50,000X magnification. Images were recorded on film and digitized.
DOI: 10.6075/j0qc02z4
title: CIL: 51800, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

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: 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: 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/j0gb23f2
title: CIL: 51150, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

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: 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: 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/j0rv0mh2
title: CIL:39089, Plasmodium yoelii nigeriensis, Anopheles stephensi, oocyst. In Cell Image Library

description: B0007349 Malaria parasites. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
description: Colorized scanning electron micrograph of malaria (Plasmodium yoelii nigeriensis) oocysts ( thick-walled structure in which sporozoan zygotes develop) developing on the midgut wall of the mosquito Anopheles.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: inelastic scattering of electrons
Source of contrast: differences in deposition of metal shadow
Visualization methods: visualization of contiguous regions
Processing history: colorized
DOI: 10.6075/j04f1q1p
title: CIL:1913, 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: 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 4 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/j0571c1s
title: CIL:35919, Saccharomyces cerevisiae. In Cell Image Library

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: 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 electrons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP-tagged TEM1. 
 
 TEM1 is a GTP-binding protein of the ras superfamily involved in termination of M-phase; controls actomyosin and septin dynamics during cytokinesis. 
 
These phase,gfp images are part of an image group that ranges from CIL:35900-35919. 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/j0tb16kt
title: CIL: 54465, Homo sapiens. In Cell Image Library

description: Imaging mode: bright-field microscopy
Visualization methods: silver nitrate and ammonium hydroxide
description: Pathology load assessment of de-identified, human, post-mortem Alzheimer's disease and age-matched non-symptomatic donor prefrontal cortex brain tissue. We used these imaging data to inform donor stratification when we generated a large single nuclei RNA sequencing (snRNA-seq) dataset. Given we generated both imaging and snRNA-seq datasets the same location/piece of tissue for each donor, this gives us an unprecedented platform to evaluate cell type/subpopulation transcriptomes and relate them directly to their respective tissue microenvironments.
description: 5 um sections of FFPE prefrontal cortex tissue from post-mortem, human Alzheimer's disease donor labeled by Bielschowsky's silver stain.
DOI: 10.6075/j0w66jh6
title: CIL:11932, Taricha granulosa, epithelial cell of lung. In Cell Image Library

description: Four general zones of f-actin movement are seen in primary cultures of newt lung epithelial cells microinjected with X-rhodamine actin. At the leading edge and throughout the lamellipodium, f-actin speckles continuously appeared and moved towards the cell center. As speckles approached the junction between the lamellipodium and lamellum they usually disappeared, F-actin underwent slower retrograde flow in the lamellum, and F-actin generally moved forward in the cell body. Time-lapse FSM was performed on a spinning disk confocal microscope system. Light from a 50 mW Krypton-Argon ion laser (Melles Griot, OmniChrome) was delivered by a single-mode fiber optic (Point Source) to a Yokogawa spinning disk confocal scan-head (Ultra-View; PerkinElmer) on an inverted microscope (TE300 Quantum; Nikon). Images were collected by a 100x 1.4NA Plan-Apo DIC objective lens (Nikon) and captured with an Orca 2 camera (Hamamatsu). Images were collected in the ventral focal plane at 10 s intervals. Images were processed as follows: (1) background subtraction; (2) 3 x3 low pass filter; (3) unsharp mask filter. Corresponds to Fig 2E and video 2 in JCB , Volume 158, Number 1, July 8, 2002 31-37
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: spinning disk confocal microscopy; fluorescent speckle microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: X-Rhodamine
Processing history: background subtraction, 3X3 low pass filter, unsharp mask
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j05b01pt
title: CIL:1125, Caenorhabditis elegans, muscle cell. In Cell Image Library

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 4 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.
DOI: 10.6075/j0tm792c
title: CIL:25399, Drosophila melanogaster, salivary gland cell. In Cell Image Library

description: Salivary glands from 3rd instar larvae of Drosophila melanogaster were dissected, fixed with formalin-acetic acid containing 0.1% Triton-X 100, and squashed on a glass slide. After freezing in liquid nitrogen, the cover slips removed, and the slide thawed and stained with 1% uranyl acetate, rinsed in 50% ethanol, dehydrated and transferred to amyl acetate, and covered with 2% parlodion in amyl acetate. Selected areas of the parlodion film, are transferred to formvar coated EM grids, and the parlodion removed by immersion in amyl acetate (see Ris H, 1981 Stereoscopic Electron Microscopy of Chromosomes, Meth Cell Biol 22:77-96). Grids were observed using the Madison High Voltage Electron Microscope at 1 MeV.
description: Preparation: formaldehyde fixed tissue; acetic acid treatment
Relation to intact cell: squashed preparation
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
description: Whole mount squash of Drosophila polytene chromosome viewed with high voltage EM showing a series of bands and interbands. This micrograph was recorded with a tilt angle of 45 degrees. The accompanying grouped image, taken at 55 degrees forms a stereo pair, providing an oblique 3D view of the chromosome.
DOI: 10.15468/dl.dy9bhh
title: Occurrence Download

description: A dataset containing 3248 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Diceros bicornis"
 ]
}

 The dataset includes 3248 records from 83 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009657-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0rn37hk
title: CIL: 53770, Homo sapiens, HeLa. In Cell Image Library

description: CMGC 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.
description: Visualization methods: confocal microscopy
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.
DOI: 10.6075/j0348j7j
title: CIL:42511, Aplysia, neuron. 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 epitope
description: Fluorescence micrograph of a neuron regenerating in culture. Honorable Mention, 2006 Olympus BioScapes Digital Imaging Competition.
DOI: 10.6075/j0js9p58
title: CIL:11502, Rattus, neuron. In Cell Image Library

description: Preparation: crosslinking-fixative fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: osmium tetroxide
Data qualification: Processed
description: Figure 291 from Chapter 10 (Lipochrome Pigment) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. Brown cytoplasmic inclusions identified as lipofuscin, or lipochrome pigment increase in number in aging cells of the brain. Image by Enrico Mugnaini. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
DOI: 10.6075/j0n58kr0
title: CIL: 50757, Drosophila melanogaster. In Cell Image Library

description: We show in this study that brain and intestinal stem cells of Drosophila contain a new type of cytoplasmic protrusion which is enriched in mitochondria and that the mitochondria are probably dependent on microtubules for their distribution. The protrusions form mitochondria-enriched cytoplasmic bridges from the stem cells to their niche that we speculate are important in regulating stem cell quiescence and activation.
description: Specimen preparation: Larval brains (LBs) were prepared from starved (amino acid-restricted) first instar (L1) larvae to enrich for quiescent neural stem cells. The LBs were glutaraldehyde-fixed, tannic acid and OsO4-stained, embedded in resin, thin-sectioned (60-70 nm) and stained with uranyl acetate/lead citrate, then observed by TEM.
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/j0pn95pn
title: CIL:10098, Rattus, multipolar neuron. In Cell Image Library

description: This multi-layer 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. 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.
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/j0ws8rvs
title: CIL:48806, Mus musculus, MC57-Cerulean. In Cell Image Library

description: Mice were euthanized and tumors were freshly explanted. 1-2 mm thick sections were cut at different depths and kept in PBS during the imaging session. Fluorescent confocal microscopy was done using a Leica SP5 II TCS tandem scanner 2-photon spectral confocal microscope with XY motorized stage, using a 25X/NA 0.95 water lens from Leica.
description: To determine the origin (local vs. circulating) of tumor associated fibroblasts, a parabiotic pair of mice was created where only one mouse expressed EGFP under the control of the type I collagen alpha-1 promoter (COL-EGFP), and the other mouse expressed DsRed ubiquitously. On each mouse of the parabiotic pair, MC57-Cerulean cancer cells were injected on the distal flank. This folder contains images from the tumor grown in the COL-EGFP mouse, freshly explanted and analyzed ex vivo. The blue channel shows cancer cells, the red channel shows DsRed cells, the green channel shows COL-EGFP+ fibroblasts
 
Image name: 120513 Parabiot Rag MC57 COLEGFP tumor flank.lif - 2 
 
Project ID: 20389
description: Item type: confocal microscopy
DOI: 10.6075/j0zp4569
title: CIL:10466, Toxoplasma gondii RH. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD); recorded
Imaging mode: 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
Visualization methods: EGFP; mCherryFP
Processing history: 3D-deconvolution
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
description: Toxoplasma gondii expressing EGFP tagged Tgbeta2-tubulin and mCherry-TgDCCP (Double cortin containing protein), an unpublished microtubule binding protein. Images overlaid with DIC. For GFP, ex 450-490 em 500-540; for mCherry ex 555-592 em 600-665. Images acquired using API Delta Vision on a Olympus ix70 wide-field microscope. Objective: Olympus 60X water immersion, 1.2 NA. Captured with CoolSnapHQ/ICX285. 23 images in z-series; this is a deconvolved stack derived from raw data: CIL# 10465.

Image is a control not treated with oryzalin. Part of an experiment with oryzalin-treatment. 

Unpublished image that is similar to images published in PMID: 16518471. See publication for other experimental details.
DOI: 10.15468/dl.brgpw3
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Astragalus dschimensis"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009658-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.