cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j05m64ws
title: CIL:14681, Oscillatoria tenuis. In Cell Image Library

description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: whole mounted tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: transmission electron microscopy (TEM)
Source of contrast: electron density
Visualization methods: shadowing and plating
Data qualification: Raw;spatialmeasurements
description: The thylakoids of the vegetative cells of the filamentous cyanobacteria, Oscillatoria tenuis, are capable of oxygen-evolving photosynthesis. Freeze-fracture replicas of the vegetative cells revealed the structure of the thylakoids. 

The process of freeze-fracture splits memebranes along their hydrophobic interior revealing two complementary fracture faces designated P-face and E-face. Each fracture faces has a population of particles which represent intramembrane proteins or protein complexes. 

Oscillatoria cultures were maintained on agar plates. Cells were collected and suspended in 10 mL dH2O, spun at 2,000 g for 10 min in a clinical centrifuge, resuspended in 5 mL dH2O. Added 5 mL 70% glycerol over 1 hr with continuous stirring, spun at 2,000 g for 10 min in a clinical centrifuge. Pellets were placed on copper support discs, frozen in liquid Freon 12 and stored under liquid nitrogen. Replicas were prepared on a Blazers BA 360 freeze-etch unit and examined in a JEOL TEM 100C at 50,000X magnification.
DOI: 10.6075/j0833qxw
title: CIL:36559, Xenopus laevis, fertilized egg. In Cell Image Library

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: 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: Images collected on a Zeiss LSM 710 confocal with a 10X 0.3 NA objective using 561 and 633 laser lines.
DOI: 10.6075/j06d5rpd
title: CIL:28768. In Cell Image Library

description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
description: One of the principal challenges in counting or segmenting nuclei is dealing with clustered nuclei. To help assess algorithms' performance in this regard, this synthetic image set consists of five subsets with increasing degree of clustering. Five subsets of 20 images each are provided. Each image contains 300 objects, but the objects overlap and cluster with overlap probability ranging from 0.0 to 0.6, and can be found with CIL 27833, 27853, 28754, 28734, and 28714, respectively. This image set has 0.30 probability overlap. The images were generated with the SIMCEP (http://www.cs.tut.fi/sgn/csb/simcep/tool.html) simulating platform for fluorescent cell population images (Lehmussola et al., IEEE T. Med. Imaging, 2007 and Lehmussola et al., P. IEEE, 2008). Ground truth for foreground/background segmentation are available as binary images as the second image in the tiff image stack. 
Recommended citation "We used the Synthetic 1 image set (Ruusuvuori et al., in Proc. of the 16th European Signal Processing Conference (EUSIPCO-2008), 2008), available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
DOI: 10.6075/j07h1hc9
title: CIL:26531, Mus musculus, fibroblast. In Cell Image Library

description: Cells were cultured in DME (Invitrogen) supplemented with 10% fetal bovine serum and 100 U/ml penicillin/streptomycin (Invitrogen) at 37°C in a humidified 5% CO2 incubator. For transfections, cells in 60-mm-diameter dishes or on fibronectin-coated coverslips were incu- bated with a mixture of DNA and LipofectAMINE 2000 (Invitrogen) according to the manufacturer's instructions. The cDNA for MLC was subcloned into pCMV-myc (Takara Bio Inc.). Mutant constructs of MLC were generated using a QuikChange site-directed mutagenesis kit (Agilent Technologies) according to the manufacturer's protocol. In this myc-tagged MLC mutant, Thr18/Ser19 were replaced by glutamic acids, and expressed in NIH3T3 cells.
In some experimental conditions, 16 h after replating onto fibronectin-coated coverslips, cells were treated with 50 ng/ml PDGF for 20 min. Cells were fixed 24–48 h after transfection using 3.7% paraformaldehyde in PBS for 15 min, permeabilized using 0.2% Triton X-100 in PBS for 2 min, blocked with 2% BSA in PBS, and co-stained for MLC (green), TRIO (red), and actin (blue). Images were captured by Zeiss LSM 710 confocal microscope with Plan-Apochromat 63X objective.
description: To study the molecular mechanism by which nonmuscle myosin II (MII) regulates protrusion and adhesion dynamics in migrating cells, NIH3T3 cells were transfected with myc-tagged phosphomimetic constitutively active MLC mutants (MLCee, green) and co-stained for TRIO (a multifunctional, multidomain Rho guanine nucleotide exchange factor, red) and filamentous actin (blue). These findings help elucidate a functional link between MII and Rac1/Cdc42 GTPases, which may regulate protrusion/adhesion dynamics in migrating cells. This image is original data from Fig. S5 "Expression of active MLC mutants inhibits the dissociation of MII–Trio complex," in J. Cell Biol. 2010. Vol. 190(4):663–674
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; distribution of a specific protein
Visualization methods: Alexa Fluor 488; Alexa Fluor 546; phalloidin
Data qualification: Raw
DOI: 10.6075/j08p605b
title: CIL: 53555. In Cell Image Library

description: AGC 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/j0tb15q6
title: CIL:10837, Perameles nasuta, epithelial cell. In Cell Image Library

description: Preparation: crosslinking-fixative fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Data qualification: Processed
description: Figure 262 from Chapter 8 (Lysosomes) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. Aggregations of primary lysosomes in the supranuclear region of an epithelial cell from the epididymis of the bandicoot, Perameles nasuta. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
DOI: 10.6075/j09p316c
title: CIL: 52311, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: One z layer of a z-stack at the given tile position
description: Tile x=4, y=2, z=13 from BL_024216_Myc_Terc
DOI: 10.6075/j08k77r6
title: CIL:28778, Caenorhabditis elegans, embryo. In Cell Image Library

description: Spinning disk confocal time-lapse imaging of the first mitosis in a C. elegans embryo expressing GFP-KNL-2 in strain OD31. As seen for GFP-CeCENP-A (CIL 28780), discrete foci of the GFP signal within the nucleus coalesce to form holocentric kinetochore plates during prophase. GFP image on left and DIC image on right. After nuclear envelope breakdown, chromosomes appear as paired lines and congress to the metaphase plate. At metaphase, sister kinetochores form two lines facing opposite spindle poles. During anaphase, foci of GFP-KNL-2 were seen to form in the spindle area. The video is ∼16 min long, and the frame is ∼30 µm top to bottom. DIC is shown on the right, and GFP is shown on the left. Images were acquired at 10-s intervals.
description: Images were acquired via a spinning disk confocal microscope (CSU10; McBain Instruments) mounted on an inverted microscope (TE2000e; Nikon). Strain TH32 coexpressing GFP-histone H2b and GFP–γ-tubulin was imaged using a 60× 1.4 NA plan Apo objective with 1.5× auxiliary magnification and a cooled CCD camera (Orca ER; Hamamatsu) binning 2 × 2. Strain OD31 expressing GFP–KNL-2 was imaged in the same manner without the 1.5× auxiliary magnification.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: spinning disk confocal 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; visualization of contiguous regions
Processing history: unprocessed raw data
DOI: 10.6075/j01j98dc
title: CIL:28774, Caenorhabditis elegans, embryo. In Cell Image Library

description: Spinning disk confocal time-lapse imaging of the first mitosis in a C. elegans embryo expressing GFP-histone and GFP-γ-tubulin (strain TH32). After finishing meiosis (not depicted), the female pronucleus migrates toward the male pronucleus (right side of the image, which is the embryo posterior), the chromosomes condense, and, after nuclear envelope breakdown, congress to the metaphase plate. Anaphase segregation of the chromosomes results in two equivalent nuclei. The video is ∼16 min long, and the frame is ∼30 µm top to bottom. DIC is shown on the left, and GFP is shown on the right. Images were acquired at 10-s intervals, and corresponding data are shown in Fig. 1 A from J Cell Biol. 2007 Mar 12;176(6):757-63. Epub 2007 Mar 5.
description: Images were acquired via a spinning disk confocal microscope (CSU10; McBain Instruments) mounted on an inverted microscope (TE2000e; Nikon). Strain TH32 coexpressing GFP-histone H2b and GFP–γ-tubulin was imaged using a 60× 1.4 NA plan Apo objective with 1.5× auxiliary magnification and a cooled CCD camera (Orca ER; Hamamatsu) binning 2 × 2. Strain OD31 expressing GFP–KNL-2 was imaged in the same manner without the 1.5× auxiliary magnification.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: spinning disk confocal 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; visualization of contiguous regions
Processing history: unprocessed raw data
DOI: 10.6075/j0h41r39
title: CIL: 54435, Homo sapiens. In Cell Image Library

description: Pathology load assessment of de-identified, human, post-mortem Alzheimer's disease and age-matched non-symptomatic donor prefrontal cortex brain tissue. We used these imaging data to inform donor stratification when we generated a large single nuclei RNA sequencing (snRNA-seq) dataset. Given we generated both imaging and snRNA-seq datasets the same location/piece of tissue for each donor, this gives us an unprecedented platform to evaluate cell type/subpopulation transcriptomes and relate them directly to their respective tissue microenvironments.
description: Imaging mode: bright-field microscopy
Visualization methods: silver nitrate and ammonium hydroxide
description: 5 um sections of FFPE prefrontal cortex tissue from post-mortem, human non-symptomatic donor labeled by Bielschowsky's silver stain.
DOI: 10.6075/j0ms3rdk
title: CIL:28779, Caenorhabditis elegans, embryo. In Cell Image Library

description: Spinning disk confocal time-lapse imaging of the first mitosis in a C. elegans embryo expressing GFP-KNL-2 in which CeCENP-A has been depleted by RNAi in strain OD31. Diffuse nuclear GFP signal is evident during prophase. However, unlike the control (CIL 28778), no discrete GFP foci were seen until anaphase onset, at which point foci of GFP-KNL-2 formed along the spindle and on the chromatin. The video is ∼18 min long, and the frame is ∼30 µm top to bottom. Images were acquired at 10-s intervals.
description: Images were acquired via a spinning disk confocal microscope (CSU10; McBain Instruments) mounted on an inverted microscope (TE2000e; Nikon). Strain TH32 coexpressing GFP-histone H2b and GFP–γ-tubulin was imaged using a 60× 1.4 NA plan Apo objective with 1.5× auxiliary magnification and a cooled CCD camera (Orca ER; Hamamatsu) binning 2 × 2. Strain OD31 expressing GFP–KNL-2 was imaged in the same manner without the 1.5× auxiliary magnification.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: unprocessed raw data
DOI: 10.6075/j03777qr
title: CIL:2878, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
description: Rabbit psoas skeletal muscle fibers were held at constant length and rigor induced by immersion in 0.2% saponin. The fibers were quick-frozen by contact with a liquid helium-cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 24 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

Images were recorded on Kodak 4489 film at 75,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:2877.
DOI: 10.6075/j0m32v05
title: CIL:239, Mus musculus, fibroblast. 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: differences in protein conformation
Data qualification: Processed
description: See P. Nalbant et al 2004. Activation of endogenous Cdc42 visualized in living cells. Science 305:1615-1619.
description: The image depicts a live neutrophil cell showing the level of activation of the signaling protein Cdc42, a member of the Rho family of small guanosine triphosphatase (GTPase) proteins which regulates multiple cell functions, including motility, proliferation, apoptosis, and cell morphology. Here, the fluorescence level is related to protein conformational changes and interactions, with warmer colors indicating higher levels of activation.
DOI: 10.6075/j00r9n26
title: CIL:28776, Caenorhabditis elegans, embryo. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: unprocessed raw data
description: Images were acquired via a spinning disk confocal microscope (CSU10; McBain Instruments) mounted on an inverted microscope (TE2000e; Nikon). Strain TH32 coexpressing GFP-histone H2b and GFP–γ-tubulin was imaged using a 60× 1.4 NA plan Apo objective with 1.5× auxiliary magnification and a cooled CCD camera (Orca ER; Hamamatsu) binning 2 × 2. Strain OD31 expressing GFP–KNL-2 was imaged in the same manner without the 1.5× auxiliary magnification.
description: Spinning disk confocal time-lapse imaging of the first mitosis in a C. elegans embryo that has been depleted of CeCENP-A by RNAi. GFP-histone and GFP-γ-tubulin were imaged (strain TH32). Pronuclear migration is normal, but chromosome condensation is disrupted. Chromosomes fail to form a proper metaphase plate, and the spindle poles move away from the chromatin masses prematurely. Anaphase segregation fails, and chromatin masses are left in the middle of the cell. The video is ∼19 min long, and the frame is ∼33 µm top to bottom. Images were acquired at 10-s intervals, and corresponding data are shown in Fig. 1A in J Cell Biol. 2007 Mar 12;176(6):757-63. Epub 2007 Mar 5.
DOI: 10.6075/j0qv3k50
title: CIL:28773. In Cell Image Library

description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
description: One of the principal challenges in counting or segmenting nuclei is dealing with clustered nuclei. To help assess algorithms' performance in this regard, this synthetic image set consists of five subsets with increasing degree of clustering. Five subsets of 20 images each are provided. Each image contains 300 objects, but the objects overlap and cluster with overlap probability ranging from 0.0 to 0.6, and can be found with CIL 27833, 27853, 28754, 28734, and 28714, respectively. This image set has 0.30 probability overlap. The images were generated with the SIMCEP (http://www.cs.tut.fi/sgn/csb/simcep/tool.html) simulating platform for fluorescent cell population images (Lehmussola et al., IEEE T. Med. Imaging, 2007 and Lehmussola et al., P. IEEE, 2008). Ground truth for foreground/background segmentation are available as binary images as the second image in the tiff image stack. 
Recommended citation "We used the Synthetic 1 image set (Ruusuvuori et al., in Proc. of the 16th European Signal Processing Conference (EUSIPCO-2008), 2008), available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
DOI: 10.15468/dl.4kszbc
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is Asia",
 "Country is Indonesia",
 "Geometry POLYGON((108.57342 2.49695,108.14194 0.33974,109.02496 -3.59136,115.92857 -4.79224,121.54779 5.38907,117.13269 7.54257,108.57342 2.49695))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Barringtonia racemosa"
 ]
}

 The dataset includes 17 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009411-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0jm2888
title: CIL:28772. In Cell Image Library

description: One of the principal challenges in counting or segmenting nuclei is dealing with clustered nuclei. To help assess algorithms' performance in this regard, this synthetic image set consists of five subsets with increasing degree of clustering. Five subsets of 20 images each are provided. Each image contains 300 objects, but the objects overlap and cluster with overlap probability ranging from 0.0 to 0.6, and can be found with CIL 27833, 27853, 28754, 28734, and 28714, respectively. This image set has 0.30 probability overlap. The images were generated with the SIMCEP (http://www.cs.tut.fi/sgn/csb/simcep/tool.html) simulating platform for fluorescent cell population images (Lehmussola et al., IEEE T. Med. Imaging, 2007 and Lehmussola et al., P. IEEE, 2008). Ground truth for foreground/background segmentation are available as binary images as the second image in the tiff image stack. 
Recommended citation "We used the Synthetic 1 image set (Ruusuvuori et al., in Proc. of the 16th European Signal Processing Conference (EUSIPCO-2008), 2008), available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
DOI: 10.6075/j0348j63
title: CIL:11443, Cyprinodon variegatus. In Cell Image Library

description: Preparation: crosslinking-fixative fixed tissue; embedded tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Data qualification: Processed
description: The internal structure of mitochondria can change in response to physiological demand. Here, after the Sheepshead minnow Cyprinodon variegatus was kept in constant light for 4 weeks, mitochondria from cells of the pseudobranch acquired an additional category of tubular cristae arranged in rows between the longitudinally oriented foliate cristae. Inset: a longitudinal section suggests these cristae have a helical tubular organization. This image, courtesy of Jospeh Harb and Eugene Copeland, appears as Figure 249 from Chapter 7 (Mitochondria) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.