cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j07943mj
title: CIL:35279, Rattus rattus, hepatocyte. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; glutaraldehyde fixed tissue
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 a specific protein
Visualization methods: Rhodamine; primary antibody plus labeled secondary antibody
Processing history: 3D-deconvolution
Data qualification: Processed;spatialmeasurements
description: Image was collected with 1 60X, 63X, or 100X oil immersion objective with a numerical aperture of 1.25 such that each pixel size was 0.23 X 0.23 um. The image was collected as part of a Z series with step size of 0.53 um. A Photometrics cooled CCD camera based on the KAF1400 chip was used.
description: Primary rat hepatocytes in culture fixed and stained for beta-tubulin. The microtubules form a network throughout the cytoplasm. In this image they are seen originating from a brighter and denser region adjacent to the cell nucleus.
 
 This is a single optical section a few microns up from the substrate collected by widefield fluorescence microscopy with a Photometrics camera with a KAF1400 chip. The imaging was performed at a microscopy course at Woods Hole Oceanographic Institute in October 1993 and deconvolved on VayTec software running on a Macintosh computer. At the time, deconvolution was new and novel for use by biologists.
DOI: 10.15468/dl.kczfuy
title: Occurrence Download

description: A dataset containing 36515 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Taxon occurrence data for the FungalRoot database"
 ]
}

 The dataset includes 36515 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009665-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0t152g7
title: CIL:41633, Juncus. In Cell Image Library

description: Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: autofluorescence
description: Fluorescence micrograph showing the cross-section of bulrush (Juncus sp.) leaf, autofluorescing red (chlorophyll on external side of leaf) and blue (vascular bundles). 
 The diameter of the stalk is approximately 3mm.Honorable Mention, 2011 Olympus BioScapes Digital Imaging Competition©.
DOI: 10.6075/j03n22pg
title: CIL:1071, 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/j04t6hr9
title: CIL:37398, damselfly, flight muscle cell. In Cell Image Library

description: The image shows the surface of the ribbon-like myofibrils, with some remnants of the SR attached mostly at the Z lines. The regular disposition of attached cross bridges is visible in many areas. Most images show fractures through the outer membrane of mitochondria and SR/T tubules of dyads nestled in long grooves of the mitochondrial surface. All leaflets of the membranes appear in the images.This image is part of the group image CFA00513 (file cfa1061.mrc to cfa1097.mrc). Negatvies scanned at LBL then reduced in size for upload TEM magnifications not currently available. Scan step size is 6.3 micron, then reduced in size 4X for upload, for an effective pixel size of 25 micron.
 
 Technical details:
 Heads and tail were removed, the thorax was bisected and immersed in 100 mM KCl, 10 mM EDTA, 10 Triton X for a few hrs, to depolarize and skin the fibers, then maintained at -20 C in 50% glycerol in the same solution for several weeks to induce rigor by eliminating ATP. The muscle was gently homogenized in a waring blender in 0.9% NaCl. The fibrils were deposited on glass and sequentially fixed in 0.1% glutaradehyde in 0.1 M cacodylate buffer, rinsed in 100 mM ammonium acetate, treated with 1% uranyl acetate for 30 seconds, rinsed in 40% methanol and frozen in liquid nitrogen. The fibrils were freeze dried at -90 C for 30 minutes and rotary shadowed with platinum either at 25C or 45C in a Balzer‚Äôs 400 freeze fracture. The glass was dissolved in hydrofluric acid and the replicas were mounted on copper grids and examined in a Philips 410 Microscope.
 
References for the image: 
Loesser, K.E. and Franzini-Armstrong, C. A simple method for freeze-drying of macromolecules and macromolecular complexes. J. Struct. Biol. 103: 48-56, 1990. Bard, F., Franzini-Armstrong, C. and Ip W. Rigor cross bridges are double headed in fast muscle from crayfish. J. Cell Biol. 105: 2225-2234, 1987.
description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: unembedded tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: digitized negative film
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0mg7ngn
title: CIL:36546, Xenopus laevis, fertilized egg. In Cell Image Library

description: This image is part of a large data set of Xenopus laevis eggs imaged at various times post fertilization (the first number of the file name corresponds minutes, eg 30_2 is 30 min post fertilization). The embryos are stained for alpha-tubulin (green) using a directly labeled B-5-1-2 antibody and DNA (red).
description: Preparation: methanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; distribution of a specific protein
Visualization methods: labeled primary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Images collected on a Zeiss LSM 710 confocal with a 10X 0.3 NA objective using 561 and 633 laser lines.
DOI: 10.6075/j0q23xzh
title: CIL:13876, Saccharomyces cerevisiae. In Cell Image Library

description: Cells (MATa tem1::TEM1-yEGFP::SpHIS5 bfa1::HIS3) were fixed in 2.5% formaldehyde for 10 min, washed twice, and resuspended in 0.1 M potassium phosphate buffer, pH 6.4. Cells were then fixed for 10 min in 80% ethanol and resuspended in 1 mg/ml DAPI. Imaging was performed at 25C using a Leica DM6000 microscope equipped with a 100x/1.40 NA oil immersion objective lens, A4, L5, and TX2 filters, and a digital CCD camera (DFC350, Leica). Pictures were processed with LAS AF (Leica) and ImageJ software.
description: Tem1 (green) loading onto spindle pole bodies during metaphase is severely affected in bfa1Δ cells. Compare with control image CIL# 13877. DAPI (blue) and DIC (hidden) are also shown. CIL# 13871 and 13870 show corresponding anaphase images. Image is Fig S4B, bottom panels, in J Cell Biol. (2011) 192: 599-614. Images in Fig S4 include CIL# 13877, 13876, 13879, 13878.
description: Preparation: formaldehyde fixed tissue; ethanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: widefield illumination; fluorescence microscopy; differential interference contrast microscopy
Parameter imaged: fluorescence emission; optical path length gradient
Source of contrast: distribution of a specific protein; compartmentalization of stain or label; boundaries between regions with different refractive index
Visualization methods: EGFP; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0j38spz
title: CIL:39967, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Wild type adult female mouse was anesthetized with nembutal, and perfused with 4% paraformaldehyde + 0.1% glutaraldehyde, followed by 1 hr. postfixation in 4% paraformaldehyde. Tissue was sectioned on a vibratome at a thickness of 80µm. Following rinses in phosphate buffer (PBS), sections were blocked (PBS with 3% NGS;1% fish gel, 0.1% Triton X-1000; 1% BSA) for 1 hour, followed by rinses in working buffer (1:10 blocking buffer: PBS). Primary antibody was diluted in working buffer (anti-alpha-SYN; Host = Rabbit used at 1:500), and tissue was covered with aluminum foil and incubated on a shaker in cold room overnight. Tissue was washed with working buffer and incubated in secondary antibody (goat anti-rabbit AlexaFluor 568, 1:50) covered with foil, on cold room shaker, 48 hrs. After rinses, 1:100 Hoescht 33342 was used to stain nuclei (30 min). After rinsing in PBS, sections were mounted on slides and coverslipped using Gelvatol. Sections were imaged using a BioRad RTS 2000MP Multiphoton, with a Nikon Plan Fluor 40X, NA 1.3 objective.
description: Image mosaic of a section through striatum showing localization of alpha synuclein in a wild type mouse. Dark area in upper right (cortex) results from unevenness in section flatness rather than lack of staining in this area. This mosaic image has been downsampled from the raw data image, which can be accessed using the link provided to the Cell Centered Database. For more information regarding this project, see: Price DL, Chow SK, MacLean NAB, Hakozaki H, Peltier S, Martone ME, Ellisman MH (2006) High-Resolution Large-Scale Mosaic Imaging using Multiphoton Microscopy to Characterize Transgenic Mouse Models of Human Neurological Disorders. Neuroinformatics. 2006;4(1):65-80.
description: Preparation: formaldehyde fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody; Alexa Fluor 568
Data qualification: Processed
DOI: 10.6075/j0251gx2
title: CIL:13872, Saccharomyces cerevisiae. In Cell Image Library

description: Cells (MATa tem1::GAL-UPL-TEM1-TRP1 bfa1::HIS3 pRS316::eGFP-TEM1-CAAX) were fixed in 2.5% formaldehyde for 10 min, washed twice, and resuspended in 0.1 M potassium phosphate buffer, pH 6.4. Cells were then fixed for 10 min in 80% ethanol and resuspended in 1 mg/ml DAPI. Imaging was performed at 25C using a Leica DM6000 microscope equipped with a 100x/1.40 NA oil immersion objective lens, A4, L5, and TX2 filters, and a digital CCD camera (DFC350, Leica). Pictures were processed with LAS AF (Leica) and ImageJ software.
description: Tem1-CAAX (green) is targeted away from spindle pole bodies in bfa1Δ cells. The CAAX motif from Ras2 targets proteins to the cytoplasmic side of the membrane. tem1Δ::GAL-UPL-TEM1 cells expressing eGFP-TEM1-CAAX from a CEN plasmid were grown on 2% raffinose/2% galactose and transferred to 2% glucose medium prior to image capture. A differential interference contrast (DIC) image is also shown (hidden). The tem1Δ::GAL1-UPL-TEM1 strain allows for the rapid, conditional depletion of Tem1. UPL, which stands for ubiquitin-proline-LacI, acts as a destabilizing module that permits rapid degradation of appended proteins. Image is Fig 7A, bottom panels, in J Cell Biol. (2011) 192: 599-614. Images in Fig 7 include CIL #13888, 13872, 13813, 13889, 13874.
description: Preparation: formaldehyde fixed tissue; ethanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: widefield illumination; fluorescence microscopy; differential interference contrast microscopy
Parameter imaged: fluorescence emission; optical path length gradient
Source of contrast: distribution of a specific protein; boundaries between regions with different refractive index
Visualization methods: EGFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0rj4h66
title: CIL:13871, Saccharomyces cerevisiae. In Cell Image Library

description: Cells (MATa tem1::TEM1-yEGFP::SpHIS5) were fixed in 2.5% formaldehyde for 10 min, washed twice, and resuspended in 0.1 M potassium phosphate buffer, pH 6.4. Cells were then fixed for 10 min in 80% ethanol and resuspended in 1 mg/ml DAPI. Imaging was performed at 25C using a Leica DM6000 microscope equipped with a 100x/1.40 NA oil immersion objective lens, A4, L5, and TX2 filters, and a digital CCD camera (DFC350, Leica). Pictures were processed with LAS AF (Leica) and ImageJ software.
description: Tem1 (green) primarily localizes to the daughter cell spindle pole body (SPB) during anaphase. Control image for CIL# 13870 in which Tem1 loading onto SPBs was severely affected in bfa1Δ cells. DAPI (blue) and DIC (hidden) are also shown. Image is Fig 6B, top panels, in J Cell Biol. (2011) 192: 599-614. Images in Fig 6 include CIL# 13869, 13868, 13871, 13870.
description: Preparation: formaldehyde fixed tissue; ethanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: widefield illumination; fluorescence microscopy; differential interference contrast microscopy
Parameter imaged: fluorescence emission; optical path length gradient
Source of contrast: distribution of a specific protein; compartmentalization of stain or label; boundaries between regions with different refractive index
Visualization methods: EGFP; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0qz28pn
title: CIL:13870, Saccharomyces cerevisiae. In Cell Image Library

description: Tem1 (green) loading onto spindle pole bodies during anaphase is severely affected in bfa1Δ cells. Compare with control image CIL# 13871. DAPI (blue) and DIC (hidden) are also shown. Image is Fig 6B, bottom panels, in J Cell Biol. (2011) 192: 599-614. Images in Fig 6 include CIL# 13869, 13868, 13871, 13870.
description: Preparation: formaldehyde fixed tissue; ethanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: widefield illumination; fluorescence microscopy; differential interference contrast microscopy
Parameter imaged: fluorescence emission; optical path length gradient
Source of contrast: distribution of a specific protein; compartmentalization of stain or label; boundaries between regions with different refractive index
Visualization methods: EGFP; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Cells (MATa tem1::TEM1-yEGFP::SpHIS5 bfa1::HIS3) were fixed in 2.5% formaldehyde for 10 min, washed twice, and resuspended in 0.1 M potassium phosphate buffer, pH 6.4. Cells were then fixed for 10 min in 80% ethanol and resuspended in 1 mg/ml DAPI. Imaging was performed at 25C using a Leica DM6000 microscope equipped with a 100x/1.40 NA oil immersion objective lens, A4, L5, and TX2 filters, and a digital CCD camera (DFC350, Leica). Pictures were processed with LAS AF (Leica) and ImageJ software.
DOI: 10.6075/j03x85rn
title: CIL:13990, Prochloron. In Cell Image Library

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.
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: 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
DOI: 10.6075/j0dj5dcg
title: CIL:13926, Homo sapiens, permanent cell line cell. In Cell Image Library

description: Human colon carcinoma HCT 116 cells were transfected with a GFP-LC3-encoding plasmid, cultured in complete medium for 24 h and treated with vehicle as a control for resveratrol or spermidine treatment in the presence of the SIRT1 inhibitor EX527 (Tocris Bioscience) for 4 h. For fluorescence microscopy determinations, cells cultured on coverslips were fixed in paraformaldehyde (4% wt/vol) for 15 min at RT, washed three times in PBS, and mounted with mounting medium (Vectashield). Confocal fluorescent images were captured using a confocal fluorescence microscope (TCS SP2; Leica) fitted with an Apochromat 63× 1.3 NA immersion objective. Images were acquired with a camera (DFC 350 FX 1.8.0; Leica) using LAS AF software (Leica) and processed with Photoshop (CS2; Adobe) software. Specifically, picture processing involved cropping of representative areas and linear adjustments of contrast and brightness and was performed using Photoshop (with equal adjustment parameters for all pictures); no explicit γ correction was used. Image: Figure 1D, bottom left panel, in Morselli et al. J Cell Biol 192: 615-629
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue; cultured cells in vitro
Item type: recorded image; charge coupled device (CCD)
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: brightness and contrast adjusted
Data qualification: Processed;intensitiesquantitation
DOI: 10.6075/j04q7sqh
title: CIL:13925, Mus musculus, skeletal muscle cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; embedded tissue; cryostat-sectioned tissue
Relation to intact cell: sectioned tissue
Item type: recorded image; charge coupled device (CCD)
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: brightness and contrast adjusted
Data qualification: Processed;intensitiesquantitation
description: Transgenic C57BL/6 mice expressing GFP-LC3 fusion protein, uninjected as control for injection with Resveratrol and/or spermidine. To avoid postmortem autophagy induction, dead mice were immediately perfused with 4% paraformaldehyde (wt/vol in PBS, pH 7.4). Tissues were then harvested and further fixed with the same solution for ≥4 h followed by treatment with 15% sucrose (wt/vol in PBS) for 4 h and with 30% sucrose (wt/vol in PBS) overnight. Tissue samples were embedded in Tissue-Tek OCT compound (Sakura) and stored at −70C. 5-µm-thick tissue sections were generated with a cryostat (CM3050 S; Leica), air dried for 1 h, washed in PBS for 5 min, dried at RT for 30 min, and mounted with Vectashield antifading medium. Confocal fluorescent images were captured using a confocal fluorescence microscope (TCS SP2; Leica) fitted with an Apochromat 40× 1.15 NA immersion objective. Images were acquired with a camera (DFC 350 FX 1.8.0; Leica) using LAS AF software (Leica) and processed with Photoshop (CS2; Adobe) software. Specifically, picture processing involved cropping of representative areas and linear adjustments of contrast and brightness and was performed using Photoshop (with equal adjustment parameters for all pictures); no explicit γ correction was used. Image: Figure 9C, middle left panel (muscle/Co), in Morselli et al. J Cell Biol 192: 615-629
DOI: 10.6075/j0tb16jc
title: CIL: 53418, Parvicorbicula socialis, Plankton. In Cell Image Library

description: 128x128 segmented image from volumetric hologram
description: Imaging mode: Holography
Visualization methods: Amplitude Mode
description: Choanoflagellate
DOI: 10.6075/j03b5z8w
title: CIL:9820, Opercularia [NCBITaxon:168247], Opercularia coarctata, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Non-contractile stalk showing the striated nature of the fibrous “straws.” TEM taken on 6/12/69 by R. Allen with Philips 300 operating at 60kV. Neg. 3,570X. Bar = 2µm. A print of the negative was scanned and processed in Photoshop. This image is suitable for qualitative analysis.There is a high resolution version of this image in the library (CIL:39169) 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; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; Print from negative scanned for Photoshop
Data qualification: Processed;spatialmeasurements
description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness.
DOI: 10.6075/j06q1vt1
title: CIL:47401, Staphylococcus aureus. In Cell Image Library

description: Relation to intact cell: intact cells-in vivo imaging
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Source of contrast: antibody labelling
Processing history: Converted from volocity to .avi
description: Mice were anesthetized with ketamine/xylazine, and then subcutaneous tissue on a dorsal flap was exteriorized. GFP staphylococcus aureus beads were inserted. Antibodies were injected into the vasculature to label neutrophils (red) and endothelial cells (blue). Blocking antibodies against the molecule Mac1 were administered after 2 hours of infection.
description: Visualization of lesions 48 hours after infection. (Figure 5 - Images of tissue lesions)