cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j09k499c
title: CIL:2686, 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: 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 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.
DOI: 10.6075/j0mw2gcg
title: CIL:1995, 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 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: 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/j00001fp
title: CIL:39377, Amorphophallus titanum. In Cell Image Library

description: Images collected on a FEI XL-30 FEG ESEM. Sample preparation protocol is available on the Dartmouth EM Facility web site at http://remf.dartmouth.edu:8080/EM-Wiki/36.
description: Preparation: glutaraldehyde fixed tissue; formaldehyde fixed tissue; critical_point dried specimen; ethanol dehydration
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in deposition of metal shadow
Visualization methods: visualization of contiguous regions; uranyl salt; gold
Processing history: unprocessed raw data
description: Scanning electron micrograph of an Amorphophallus titanum anther. This longitudinal section shows the locule (cavity where the pollen is located).This image is part of a group that includes CIL: 39377- 39384.
DOI: 10.6075/j0416wqg
title: CIL: 53341, Drosophila melanogaster, Entire Organism. In Cell Image Library

description: Imaging mode: Gray Scale
Visualization methods: 20x magnification captured by one of the following eyepiece cameras: Swiftcam 3 Megapixel, OMAX 9.0 MP, AmScope MU300
description: Video of Fruit Fly embryonic development. Each video is labeled with the temperature (Celcius) at which it was captured as well as the embryo name (A, B, etc)
DOI: 10.6075/j04j0d4z
title: CIL:2781, 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 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.
DOI: 10.6075/j05b02h0
title: CIL:35865, Saccharomyces cerevisiae. In Cell Image Library

description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP-tagged WHI5. WHI5 is a repressor of G1 transcription that binds to SCB binding factor (SBF) at SCB target promoters in early G1; phosphorylation of Whi5p by the CDK, Cln3p/Cdc28p relieves repression and promoter binding by Whi5; periodically expressed in G1.These phase,gfp images are part of an image group that ranges from CIL:35860-35879. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors 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 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 photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
DOI: 10.6075/j02n511c
title: CIL:24816, 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: Intracellular localization of GFP-Vps74 in BY4742 sac1∆ vps74∆ mutant. SAC1 encodes an integral membrane phosphoinositide phosphatase and in the sac1∆ vps74∆ mutant, GFP-Vps74 localizes, in addition to the Golgi apparatus, to nuclear ER and cortical ER and/or PM. Control image for images showing ectopic expression of GFP-Vps74 with mutations in the sulfate-binding pocket (CIL# 24817, 24818). This study demonstrates that the sulfate-binding pocket of Vps74 and GOLPH3 mediates PtdIns4P-binding and is essential for function. 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 Fig4A wild-type/sac1∆ panel in J Cell Biol. 187: 967-975. 2009. Images in Fig 4A include CIL#s 13449, 13451, 13453, 13455, 13456, 13457, 24816, 24817, 24818, 24819, 24820, 24821.
DOI: 10.6075/j0sq8z7k
title: CIL:41824, Drosophila melanogaster, muscle cell, sensory neuron. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Processing history: projection of confocal stacks
description: Confocal image stacks of Drosophila (fruit fly) larva with labeled dendrite arborization sensory neurons and epidermal cells. Green is dendrites of sensory neurons on the body wall and red is attachment sites of body wall muscles. This image is also part of a composite image of multiple larvae available as CIL 41825. Honorable Mention, 2010 Olympus BioScapes Digital Imaging Competition©.
DOI: 10.6075/j0wh2nvh
title: CIL:41020, Penium. In Cell Image Library

description: Unicellular alga Penium, treated with the microtubule poison 
 oryzalin. Fifth Prize, 2009 Olympus BioScapes Digital Imaging Competition©.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
DOI: 10.6075/j0sf2vvc
title: CIL: 53614. In Cell Image Library

description: Atypical 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/j0np23r3
title: CIL:37373, 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/j0k64h83
title: CIL:10492, Toxoplasma gondii RH. In Cell Image Library

description: A monolayer of human foreskin fibroblast cells was infected with Toxoplasma gondii expressing EGFP-tagged TgCentrin2 and mCherry-tagged TgDLC (dynein light chain). 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. Deconvolved stack corresponds to raw data stack: CIL# 10491. 

Unpublished image
Similar to images published in PMID: 16518471
See publication for other experimental details
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
Processing history: 3D-deconvolution
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0348k0t
title: CIL: 53348, Drosophila melanogaster, Entire Organism. In Cell Image Library

description: Imaging mode: Gray Scale
Visualization methods: 20x magnification captured by one of the following eyepiece cameras: Swiftcam 3 Megapixel, OMAX 9.0 MP, AmScope MU300
description: Video of Fruit Fly embryonic development. Each video is labeled with the temperature (Celcius) at which it was captured as well as the embryo name (A, B, etc)
DOI: 10.6075/j0930sd5
title: CIL:732, Chlorocebus sabaeus. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: living tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: EGFP
Visualization methods: UV/visible/IR photons
description: COS 7 cell expressing Organelle LightsTM Golgi-GFP (Invitrogen)consisting of the human Golgi-resident enzyme N-acetylgalactosaminyltransferase 2. Images were collected with a 63X1.4 NA Plan-Apochromat oil objective on a Zeiss LSM510 META (Carl
Zeiss, Thornwood, NY) using 488 nm excitation, HFT 488 dichroic, and LP505 emission filter. Image size is 512 x 512, pixel size is 0.1 µm
x 0.1 µm and pixel time was set to 1.6 ¬µsec. Detector pinhole was setto collect 26 ~0.5 µm slices at 0.5 µm intervals.
DOI: 10.6075/j0kp814v
title: CIL:35384, Homo sapiens, cevical carcinoma. In Cell Image Library

description: Whole human female metaphase chromosome from metaphase arrested cell swollen in hypotonic medium and treated to remove histones. The resulting residual chromosome 'scaffold' was imaged at 1 MeV. This image was taken with a specimen tilt of 45 degrees. Grouped with it is an image of the same area at 55 degrees tilt, providing an oblique stereo view of the chromosome.
description: HeLa cells were metaphase-arrested by a 3hr treatment with colcemid, the cells mechanically broken by passage through a 22-gauge needle, exposed to hypotonic 75 mM KCl for 10 min. Samples were fixed with 3:1 methanol:acetic, treated to remove histones, spread on a water surface, picked up on formvar coated grids, critical point dried, and imaged with the Wisconsin HVEM at 1 MeV. See Ris (1978) Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:229-246; Ris (1981) Stereoscopic microscopy of chromosomes. Meth Cell Biol 22:77-96.
description: Preparation: coagulating-fixative fixed tissue; critical_point dried specimen
Relation to intact cell: whole mounted tissue
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
DOI: 10.6075/j0kk9bhv
title: CIL: 54564, Xenopus Laevis, Entire Organism. In Cell Image Library

description: Imaging mode: RGB
Visualization methods: Captured on a microscope using a Canon Rebel Ti5/6 or a one of the following eyepiece cameras: Swiftcam 3 Megapixel, OMAX 9.0 MP, AmScope MU300
description: 10.3 degrees C
description: Video of African clawed frog embryonic development. Video filename format is as follows organism_temperature_batch. Data was collected at 10.3 degrees Celcius
DOI: 10.6075/j0vd6xrn
title: CIL:2187, 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/j0kh0mr6
title: CIL: 51275, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

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
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.
DOI: 10.6075/j08k78b7
title: CIL:1920, 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: 10.57745/heeyc5
title: 5_N_mineralization_rate-1.tab

description: nitrogen mineralization rate
DOI: 10.6075/j03b5z1r
title: CIL:45002, Philodina roseola, oocyte. In Cell Image Library

description: This is a live image of the bdelloid rotifer Philodina roseola under 20x magnification. Bdelloid rotifers are microscopic freshwater invertebrates best known for their capacity to undergo frequent cycles of desiccation and rehydration, their long-term asexuality, which is manifested in the absence of males and meiosis, and the ability to capture foreign genetic material at levels unprecedented in metazoans. This image of an adult female emphasizes characteristic structures such as the ciliary ring, or corona, the pharynx with a mastax consisting of hard jaws (trophi), a set of circular and longitudinal muscles, bilateral ovaries with oocyte nuclei, and the parthenogenetically developing egg. The birefringence picture was taken with new video enhanced polychromatic polscope. An eye or camera can directly see the colored polarization image in real time through the ocular with brightness corresponding to retardance and color corresponding to the slow axis azimuth. Image size is 400x240µm.
description: Preparation: living tissue
Item type: recorded image
Imaging mode: polarized light illumination
Parameter imaged: retardance
Source of contrast: intrinsic birefringence
DOI: 10.57745/w1f3yo
title: 4_mineralized_N.tab

description: mineralized nitrogen
DOI: 10.57745/kyy7mx
title: 2_bulk_density.tab

description: soil bulk density
DOI: 10.57745/nrpw4x
title: 3_microbial_biomass.tab

description: microbial biomass carbon