cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0571bbd
title: CIL:37392, 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/j0862fws
title: CIL: 52008, Homo sapiens. In Cell Image Library

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
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: 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.
DOI: 10.6075/j0kk99hf
title: CIL:13903, Caenorhabditis elegans, embryo. In Cell Image Library

description: Representative image indicative of autophagic activity of C. elegans [VC199, sir-2.1(ok434)IV] embryo expressing a full-length plgg-1DsRED::LGG-1 fusion fed with UV-killed Escherichia coli with additional 0.2 mM spermidine. Epifluorescence microscopy was performed with a microscope (AxioImager Z2; Carl Zeiss, Inc.) using a Plan Neofluar 40× objective with a 0.75 NA and a 63× Plan Neofluar objective with an NA of 1.25 in oil at RT using a 540 ± 15–nm band-pass excitation filter and a 575-nm long-pass emission filter. Images were taken with a camera (AxioCam MRc5; Carl Zeiss, Inc.) with Axiovision software (Carl Zeiss, Inc.) without further processing. Image: Figure 3A, bottom right panel, in Morselli et al. J Cell Biol 192: 615-629
description: 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: DsRed
Data qualification: Raw;intensitiesquantitation
DOI: 10.6075/j0vh5mkb
title: CIL:13461, Saccharomyces cerevisiae S288c. In Cell Image Library

description: Kre2-GFP is not efficiently maintained in the Golgi apparatus when Pik1-mediated PtdIns4P synthesis (the Golgi-localized PtdIns 4-kinase in yeast is composed of the Pik1 catalytic subunit and a myristoylated calcium-binding protein, Frq1) ceases, implicating Pik1 signaling in retrograde trafficking of Golgi residents. In this image, Kre2-GFP is expressed in the frq1-1 mutant strain after shift to restrictive temperature of 37C for 1h. 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 Fig4D 37C frq1-1 panel in J Cell Biol. 187: 967-975. 2009. Images in Fig 4D include CIL#s 13460, 13461, 13462, 13463, 13464, 13465, 13466, 13467.
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
DOI: 10.6075/j0pg1qdx
title: CIL:13901, Saccharomyces cerevisiae S288c. In Cell Image Library

description: Saccharomyces cerevisiae (WT BY4741-MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0) undergoing chronological aging on small synthetic 2% glucose media (SMD) without spermidine supplementation. Image represents EGFP-Atg8p localization, visualized by fluorescence microscopy. Yeast cells undergoing autophagy exhibit a prominent vacuolar localization of EGFP-Atg8p. Epifluorescence image was captured using a widefield microscope (Axioskop; Carl Zeiss, Inc) fitted with a Plan Neofluar 63× 1.25 NA oil immersion objective. Image acquired with a camera (SPOT 9.0 Monochrome 6; Diagnostic Instruments, Inc) using Metamorph software (Universal Imaging Corp) and processed with IrfanView and Photoshop (CS2; Adobe) software. Specifically, picture processing involved coloring and cropping of representative areas and was performed with IrfanView. In addition, linear adjustments of contrast and brightness were applied with Photoshop (using equal adjustment parameters for all pictures); no explicit γ correction was used. Image: Figure 2A, WT/Co/EGFP-Atg8p panel, in Morselli et al. J Cell Biol 192: 615-629
description: 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
Processing history: brightness and contrast adjusted
Data qualification: Processed;intensitiesquantitation
DOI: 10.6075/j00c4tgz
title: CIL:13897, Saccharomyces cerevisiae. In Cell Image Library

description: Cells (MATa tem1::KanMX ura3::eGFP-CNM67–TEM1::URA3 kin4::TRP1-pGAL1-10-KIN4) were grown in YPD (containing glucose). Imaging was performed at 25C using a Leica DM6000 microscope equipped with a 100x/1.40 NA oil immersion objective lens, and a digital CCD camera (DFC350, Leica). Pictures were processed with LAS AF (leica) and ImageJ software.
description: Preparation: living tissue
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
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: DIC image of cells constitutively expressing Tem1 localized to both spindle pole bodies (SPBs) and expressing Kin4 from the GAL1-10 promoter growing in medium with glucose. This is the control image for CIL# 13896 in which constitutive loading of Tem1 to SPBs allowed cells to progress through the cell cycle despite Kin4 overexpression. Image is Fig 5C bottom left panel in J Cell Biol. (2011) 192: 599-614. Other images in Fig 5 include CIL# 13895, 13894, 13897, 13896.
DOI: 10.6075/j0h130q0
title: CIL:13895, Saccharomyces cerevisiae. In Cell Image Library

description: DIC image of cells expressing Kin4 from the GAL1-10 promoter and growing in medium with glucose. This is the control image for CIL# 13894 in which overexpression of Kin4 arrests cells in anaphase. Image is Fig 5C top left panel in J Cell Biol. (2011) 192: 599-614. Other images in Fig 5 include CIL# 13895, 13894, 13897, 13896.
description: Preparation: living tissue
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
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Cells (MATa kin4::TRP1-pGAL1-10-KIN4) were grown in YPD (containing 2% glucose). Imaging was performed at 25C using a Leica DM6000 microscope equipped with a 100x/1.40 NA oil immersion objective lens, and a digital CCD camera (DFC350, Leica). Pictures were processed with LAS AF (leica) and ImageJ software.
DOI: 10.6075/j0jd4vh4
title: CIL:13894, Saccharomyces cerevisiae. In Cell Image Library

description: Preparation: living tissue
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
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: DIC image of cells expressing Kin4 from the GAL1-10 promoter and growing in medium with galactose. Overexpression of Kin4 arrests cells in anaphase. Compare with control image CIL# 13895. Image is Fig 5C top right panel in J Cell Biol. (2011) 192: 599-614. Other images in Fig 5 include CIL# 13895, 13894, 13897, 13896.
description: Cells (MATa kin4::TRP1-pGAL1-10-KIN4) were grown in rich media containing 2% galactose/2% raffinose. Imaging was performed at 25C using a Leica DM6000 microscope equipped with a 100x/1.40 NA oil immersion objective lens, and a digital CCD camera (DFC350, Leica). Pictures were processed with LAS AF (leica) and ImageJ software.
DOI: 10.6075/j0pv6j3h
title: CIL:13910, 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 µM Resveratrol 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, top middle 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/j0j101wt
title: CIL:13907, Homo sapiens, permanent cell line cell. In Cell Image Library

description: Human colon carcinoma HCT 116 cells were transfected with an siRNA specific for SIRT1 and then retransfected with a GFP-LC3-encoding plasmid, cultured in complete medium for 24 h and treated with 100 µM resveratrol 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 1A, bottom middle 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/j0fb52pm
title: CIL: 54360. 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: 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.
description: Visualization methods: confocal microscopy
DOI: 10.6075/j0513xb4
title: CIL:19336, Naegleria fowleri, cell by organism, eukaryotic cell, Eukaryotic Protist, Amoeboid Protist. In Cell Image Library

description: Naegleria fowleri is a free living amoebae that can be an opportunistic pathogen, and in some cases, has been diagnosed as the causative agent of the usually fatal amebic encephalitis. Other opportunistic pathogens are Balamuthia and Acanthamoeba. Naegleria and Acanthamoeba feed by phagocytosis. Balamuthia feed by inserting the tips of their pseudopodia into cells. Balamuthia and Acanthamoeba, are the linked video group.

The cells were grown in axenic media. Then they were photographed with a Canon Power Shot G3 with a setting at ISO 50 with an optical microlens at 4X and the quality set at RAW. The camera was attached to the phototube of the microscope with a 3X lens and photographed in phase contrast with a 100X oil immersion objective. Live amoebae were placed in a chamber prepared by inverting a coverslip with/or without cultured mammalian cells onto a 3X1 inch microscope slide with a thin rim of Vaseline; melted paraffin was brushed around the edge of the coverslip to seal it to the slide. Such cultures could be maintained for several days at room temperature.
description: Preparation: living tissue
Relation to intact cell: living tissue; whole mounted tissue
Item type: microscopy; in-focus phase contrast
Imaging mode: retardance; phase contrast microscopy
Parameter imaged: boundaries between regions with different refractive index
Source of contrast: boundaries between regions with different refractive index
Visualization methods: natural boundaries
Processing history: living tissue; recorded image; charge coupled device (CCD)
Data qualification: Raw
DOI: 10.6075/j0vq31tr
title: CIL:13995, Prochloron. In Cell Image Library

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.
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/j0z31xd3
title: CIL:13924, Homo sapiens, permanent cell line cell. In Cell Image Library

description: Image indicative of 24 h autophagic activity of human colon carcinoma HCT 116 cell co-transfected with a RFP-LC3-encoding plasmid and an empty vector (pcDNA3) as a control. 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 8C, top 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: Red fluorescent proteins from Anthozoa
Processing history: brightness and contrast adjusted
Data qualification: Processed;intensitiesquantitation
DOI: 10.6075/j08w3csw
title: CIL: 52063, Homo sapiens. In Cell Image Library

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
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: 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.
DOI: 10.6075/j0nv9gzq
title: CIL:13916, Mus musculus, cardiac muscle cell. In Cell Image Library

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, top left panel heart/Co), in Morselli et al. J Cell Biol 192: 615-629
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