cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j05b01cs
title: CIL:35401, Drosophila melanocephala, salivary gland. In Cell Image Library

description: Preparation: chemically fixed tissue; coagulating-fixative fixed tissue
Relation to intact cell: whole mounted tissue; chromosome squash
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: High Voltage (1MeV) TEM image of a squash preparation of polytene chromosomes from salivary gland of 3rd instar larva of Drosophila melanogaster showing the band-interband organization.
description: Salivary glands were dissected, exposed to 0.07 M KCl, fixed in 3:1 acetic acid:ethanol and squashed in 50% acetic acid. Slides were frozen in liquid nitrogen, the cover slip removed, and the slide immersed in 1% uranyl acetate for 5 min followed by dehydration in ethanol and transfer to amyl acetate. 2% parlodion in amyl acetate was spread over the slide and allowed to air dry. Areas for observation were scored, released by water immersion, picked up on formvar-coated grids and observed with the Wisconsin HVEM at 1 MeV. See Ris, H 1981 Stereoscopic Electron Microscopy of chromosomes. Meth Cell Biol 22:77-96; Ris, H 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:229-246.
DOI: 10.6075/j0cj8c73
title: CIL:13741, Drosophila melanogaster, germ line cell, follicle cell, germ line stem cell, follicle stem cell. In Cell Image Library

description: Boi (red) localizes predominantly to apical cells in Drosophila wild-type germaria but not in germaria with UAS-boi[RNAi] expression (CIL#13742). Germ cells are identified using anti-Vasa (blue). Image is Fig 2D in J Cell Biol. 2010. 191: 943-952. Other images in Fig 2 include CIL# 13738, 13739, 13740, 13741, 13742).
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
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 a specific protein
Visualization methods: primary antibody plus labeled secondary antibody; Cy3; Cy5
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Fly ovaries were dissected and fixed as described previously (O'Reilly et al., 2008). Primary antibodies were 1:50 rat-antiBoi (Hartman et al. 2010) 1:2,000 rabbit anti-Vasa (Hay et al., 1990); Secondary antibodies used were Cy3 and Cy5 conjugated to species-specific secondary antibodies (Jackson ImmunoResearch Laboratories, Inc.). Samples were mounted in Vectashield mounting medium. Images were collected at room temperature (22C) using 40× (1.25 NA) or 63× (1.4 NA) oil immersion lenses (Leica) on an upright microscope (DM 5000; Leica) coupled to a confocal laser scanner (TCS SP5; Leica). LAS AF SP5 software (Leica) was used for data acquisition. Images representing individual channels of single confocal slices from the center of each germarium were exported as TIFF files, and images were converted to figures using Photoshop software (Adobe).
DOI: 10.6075/j0z0378r
title: CIL:9692, Paramecium multimicronucleatum, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Paramecium multimicronucleatum - Video of the Contractile Vacuole Complex. In vivo CVC filling/expulsion cycles. A CV in a compressed cell is observed in side view undergoing cycles of filling (diastole) and expulsion (systole) of its fluid content as the CV membrane fuses then separates from the plasma membrane and with one radial arm. The radial arm fuses with the CV after systole then just before systole it again separates from the CV. As the CV empties fluid will flow into the end of the radial arm next to the CV that is called the ampullus. This fluid comes from the collecting canal of the same radial arm. There are actually 5 to 10 radial arms connected to one CV but the others are out of the focus plane or out of the field of focus. Movies were taken by Dr. Tomomi Tani with differential interference contrast optics attached to a Leica DMIRB inverted microscope. A Leica Fluotar x63 objective lens (NA = 0.7) was used. A DVD resolution version of this is available at CIL:10411.
description: Preparation: living tissue
Relation to intact cell: compressed living tissue
Item type: microscopy; modes of light microscopy
Imaging mode: differential interference contrast microscopy
Parameter imaged: refractive index
Source of contrast: boundaries between regions with different refractive index
Visualization methods: miscellaneous fill
Processing history: film; unprocessed raw data
DOI: 10.6075/j0833qq6
title: CIL:13740, Drosophila melanogaster, germ line cell, follicle cell, germ line stem cell, follicle stem cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
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 a specific protein
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Boi (green) no longer localizes predominantly to apical cells in Drosophila boi[e] mutant germaria (compare with CIL# 13739). Germ cells are identified using anti-Vasa (blue). Image is Fig 2C in J Cell Biol. 2010. 191: 943-952. Other images in Fig 2 include CIL# 13738, 13739, 13740, 13741, 13742).
description: Fly ovaries were dissected and fixed as described previously (O'Reilly et al., 2008). For anti-Boi immunostaining, ovaries were fixed in 2% formaldehyde on ice. Primary antibodies were 1:50 rat-antiBoi (Hartman et al. 2010) 1:2,000 rabbit anti-Vasa (Hay et al., 1990); Secondary antibodies used were FITC, Cy3, and/or Cy5 conjugated to species-specific secondary antibodies (Jackson ImmunoResearch Laboratories, Inc.). Samples were mounted in Vectashield mounting medium. Images were collected at room temperature (22C) using 40× (1.25 NA) or 63× (1.4 NA) oil immersion lenses (Leica) on an upright microscope (DM 5000; Leica) coupled to a confocal laser scanner (TCS SP5; Leica). LAS AF SP5 software (Leica) was used for data acquisition. Images representing individual channels of single confocal slices from the center of each germarium were exported as TIFF files, and images were converted to figures using Photoshop software (Adobe).
DOI: 10.6075/j0tm78wq
title: CIL:13739, Drosophila melanogaster, germ line cell, follicle cell, germ line stem cell, follicle stem cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
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 a specific protein
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Boi (green) localizes predominantly to apical cells in Drosophila wild-type germaria but not in boi[e] mutant germaria (CIL#13740). Germ cells are identified using anti-Vasa (blue). Image is Fig 2B in J Cell Biol. 2010. 191: 943-952. Other images in Fig 2 include CIL# 13738, 13739, 13740, 13741, 13742).
description: Fly ovaries were dissected and fixed as described previously (O'Reilly et al., 2008). Primary antibodies were 1:50 rat-antiBoi (Hartman et al. 2010) 1:2,000 rabbit anti-Vasa (Hay et al., 1990); Secondary antibodies used were FITC, Cy3, and/or Cy5 conjugated to species-specific secondary antibodies (Jackson ImmunoResearch Laboratories, Inc.). Samples were mounted in Vectashield mounting medium. Images were collected at room temperature (22C) using 40× (1.25 NA) or 63× (1.4 NA) oil immersion lenses (Leica) on an upright microscope (DM 5000; Leica) coupled to a confocal laser scanner (TCS SP5; Leica). LAS AF SP5 software (Leica) was used for data acquisition. Images representing individual channels of single confocal slices from the center of each germarium were exported as TIFF files, and images were converted to figures using Photoshop software (Adobe).
DOI: 10.6075/j03r0s3t
title: CIL:1795, 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 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/j0m907kn
title: CIL:36775, Paramecium caudatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Cross section of the oral region (buccal cavity) posterior to the vestibulum. The cytopharynx is beginning on the dorsal surface and the ribbed wall, peniculi and quadrulus are present on the right and left. The floor of the buccal cavity is bordered by the filamentous reticulum and an anarchic field of basal bodies is found where the endoral membranelle terminates. TEM taken on 1/31/74 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 6,150X. Bar = 1µm.
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. There is a high resolution version of this image in the library (CIL:39158) which 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; uranyl salt; lead salt; osmium tetroxide
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed
DOI: 10.6075/j02z14vz
title: CIL:2056, 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 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/j0xd10w0
title: CIL:2265, 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 6 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/j0sb4586
title: CIL: 52181, 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: 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.
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
DOI: 10.6075/j0h41qb1
title: CIL:36121, damselfly, flight muscle cell. In Cell Image Library

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
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
DOI: 10.6075/j0z036vz
title: CIL:13744, Drosophila melanogaster, germ line cell, follicle cell, germ line stem cell, follicle stem cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
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 a specific protein
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Fly ovaries were dissected and fixed as described previously (O'Reilly et al., 2008). For anti-Boi immunostaining, ovaries were fixed in 2% formaldehyde on ice. Primary antibodies were 1:50 rat anti-Boi (Hartman et al., 2010); 1:100 goat anti-Hh (Santa Cruz Biotechnology, Inc.) or 1:100 rabbit anti-Hh (Ballet et al. 2003). Secondary antibodies used were FITC, Cy3, and/or Cy5 conjugated to species-specific secondary antibodies (Jackson ImmunoResearch Laboratories, Inc.). Samples were mounted in Vectashield mounting medium. Images were collected at room temperature (22C) using 40× (1.25 NA) or 63× (1.4 NA) oil immersion lenses (Leica) on an upright microscope (DM 5000; Leica) coupled to a confocal laser scanner (TCS SP5; Leica). LAS AF SP5 software (Leica) was used for data acquisition. Images representing individual channels of single confocal slices from the center of each germarium were exported as TIFF files, and images were converted to figures using Photoshop software (Adobe).
description: Boi (green) and Hedgehog (Hh, red) are expressed in apical cells of the Drosophila wild-type germarium. In the absence of boi (boi[e] mutant), Hh is redistributed from apical cells to the extracellular space of the local follicle stem cell niche (CIL# 13745). Expression of Boi in apical cells in the boi[e] mutant rescues Hh localization to apical cells (CIL# 13746). Image is Fig 3A in J Cell Biol. 2010. 191: 943-952. Images in Fig 3 include CIL# 13744, 13745, 13746, 13747, 13748.
DOI: 10.6075/j0513x0n
title: CIL:13747, Drosophila melanogaster, germ line cell, follicle cell, germ line stem cell, follicle stem cell. In Cell Image Library

description: Fly ovaries were dissected and fixed as described previously (O'Reilly et al., 2008). For anti-Boi immunostaining, ovaries were fixed in 2% formaldehyde on ice. Primary antibodies were 1:50 rat anti-Boi (Hartman et al., 2010); 1:100 goat anti-Hh (Santa Cruz Biotechnology, Inc.) or 1:100 rabbit anti-Hh (Ballet et al. 2003). Secondary antibodies used were FITC, Cy3, and/or Cy5 conjugated to species-specific secondary antibodies (Jackson ImmunoResearch Laboratories, Inc.). Samples were mounted in Vectashield mounting medium. Images were collected at room temperature (22C) using 40× (1.25 NA) or 63× (1.4 NA) oil immersion lenses (Leica) on an upright microscope (DM 5000; Leica) coupled to a confocal laser scanner (TCS SP5; Leica). LAS AF SP5 software (Leica) was used for data acquisition. Images representing individual channels of single confocal slices from the center of each germarium were exported as TIFF files, and images were converted to figures using Photoshop software (Adobe).
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
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 a specific protein
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Boi (green) and Hedgehog (Hh, red) are expressed in apical cells of the Drosophila wild-type germarium (CIL#13744). In the absence of boi (boi[e] mutant), Hh is redistributed from apical cells to the extracellular space of the local follicle stem cell niche (CIL# 13745). Expression of Boi in apical cells relocalizes Hh to apical cells (CIL#13746), but expression of Boi[∆FN1] that lacks the Hh-binding domain fails to rescue Hh localization (this image; boi[e]; UAS-Boi[∆FN1]/+;babGal4/+). Image is Fig 3D in J Cell Biol. 2010. 191: 943-952. Images in Fig 3 include CIL# 13744, 13745, 13746, 13747, 13748.
DOI: 10.15468/dl.tasq3h
title: Occurrence Download

description: A dataset containing 15694 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Australia",
 "Geometry POLYGON((138.19335 -25.77488,135.14109 -41.60407,149.23119 -45.65009,156.2585 -25.81037,138.19335 -25.77488))",
 "TaxonKey is Eucalyptus camaldulensis"
 ]
}

 The dataset includes 15694 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009223-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.