cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0k35ssg
title: CIL:9693, Coleps hirtus, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: A print of the negative was scanned and processed in Photoshop. This image is best used for qualitative analysis. A high resolution image is in the library at (CIL:38828). Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information is available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment
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: film; Print from negative scanned for Photoshop.
Data qualification: Processed;spatialmeasurements
description: Overview of Coleps hirtus cell seen in this median transverse section. This barrel-shaped cell has a few rows of cilia and the cell is covered with calcified polysaccharide platelets that are housed within the alveoli. In this TEM the platelets are absent as they dissolved during preparation for electron microscopy. The macronucleus, a food vacuole, and a large empty vacuole is evident. Typical ciliate cytoplasm is present. TEM taken on 5/3/69 by R. Allen with Philips 300 operating at 60kV. Neg. 3,120X. Bar = 2µm.
DOI: 10.5281/zenodo.17398828
title: Waterscape dataset of the municipality of Girona
DOI: 10.5281/zenodo.17398829
title: Waterscape dataset of the municipality of Girona
DOI: 10.6075/j0nk3dnt
title: CIL: 52970, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Image 4, z=21 from SC_011
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 image
DOI: 10.6075/j0p55nm6
title: CIL:35712, Saccharomyces cerevisiae. In Cell Image Library

description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP-tagged NET1. 
 
 NET1 is a core subunit of the RENT complex that involves in nucleolar silencing and telophase exit; stimulates transcription by RNA polymerase I and regulates nucleolar structure.
 
These phase,gfp images are part of an image group that ranges from CIL:35700-35719. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the Library.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission; elastic scattering of photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
description: Time-lapse images were collected on a DeltaVision system (Olympus IX71) with 60x/1.42 NA objective at 5 minute intervals. Please see the microscopy section in the referenced manuscript for details for image analysis.
DOI: 10.6075/j0z89bmh
title: CIL:1939, Caenorhabditis elegans. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 4 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
DOI: 10.6075/j0416w8n
title: CIL:19337, Balamuthia mandrillaris, cell by organism, eukaryotic cell, Eukaryotic Protist, Amoeboid Protist. In Cell Image Library

description: Balamuthia mandrillaris was isolated from a sample of soil from a plant in the home of a child who died of amebic encephalitis. 

These free living amoebae can be opportunistic pathogens, and in some cases have been diagnosed as the causative agent of the usually fatal amebic encephalitis. Other opportunistic pathogens are Naegleria and Acanthamoeba which feed by phagocytosis. Balamuthia feed by inserting the tips of their pseudopodia into cells. The other members of opportunistic pathogens, Naegleria and Acanthamoeba, are linked to this movie.

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. Further details are available in the attached publication.
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/j08p5zjg
title: CIL:2581, Caenorhabditis elegans. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 10 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
DOI: 10.6075/j0g44p56
title: CIL:24786, Xenopus laevis, keratocyte. In Cell Image Library

description: Multiple branching of actin filaments in lamellipodia of Xenopus keratocytes. This image shows an overview of the leading edge, and CIL 24787 shows enlargements of local regions of this platinum replica. CIL 24788 shows a similar overview for the lamellipodia of a vertebrate fibroblasts. Image corresponds to Figure 1a from J Cell Biol. 1999 May 31;145(5):1009-26.
description: Preparation: permeabilized tissue; glutaraldehyde fixed tissue; phalloidin; polyethylene glycol
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: optical path length gradient
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating; platinum replica
Processing history: unprocessed raw data
description: Procedures for detergent extraction, immunostaining, S1 decoration, light, and EM were described previously (Svitkina et al., 1995, 1996, 1997;Verkhovsky et al., 1995; Svitkina and Borisy, 1998).
DOI: 10.6075/j0tq60pc
title: CIL:19326, Acanthamoeba castellanii, cell by organism, eukaryotic cell, Eukaryotic Protist, Amoeboid Protist. In Cell Image Library

description: Acanthamoeba castellani is a free living amoebae found in soil and water and can be an opportunistic pathogen as well. They have been diagnosed as the causative agent associated with keratitis, an infection of the eye, in humans. Other opportunistic pathogens are Naegleria and Balamuthia which have been associated with amebic encephalitis. Acanthamoeba and Naegleria feed by phagocytosis while Balamuthia feed by inserting the tips of their pseudopodia into cells. The other members of the video group, Naegleria and Balamuthia, are linked to this movie.

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/j0x92bcr
title: CIL:12551, Rattus, multipolar neuron. In Cell Image Library

description: Presynaptic contacts are abundant on both cell bodies and the dendritic arbor of cultured hippocampal neurons after 15 days in vitro. Neurons were immunostained for MAP2, a microtubule associated protein localized to dendrites (green) and synapsin I (red), a presynaptic vesicle protein. With the exception of the immunostained presynaptic terminals, axons are not visible in this preparation. A relatively low power objective (20X) was used to capture the entire dendritic arbor of individual cells.
Detailed methods: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained for MAP2 (monoclonal HM2, Sigma, with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and synapsin I (from P. DeCamilli, with DyLight549 conjugated secondary, excitation, 555, emission, 568, [Jackson Immunoresearch]). Images were acquired with a Leica DMRA microscope with a 20X (HC Fluotar, NA 0.5) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. Individual images of each fluorophore were colorized and assembled as a a stack file using MetaMorph software.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dissociated postmitotic neuron grown in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0c24wnb
title: CIL:54899, Homo sapiens, pyramidal cell. In Cell Image Library

description: We examined the structural organization of cytoskeletal components and membrane systems in neurons of well preserved biopsy material from Alzheimer’s disease (AD). Information was obtained from thin sectioned material using conventional electron microscopy and from thick sections with the high voltage electron microscope.
description: Imaging mode: Electronic tomography
description: This image displays the PHF array.
DOI: 10.6075/j0tq60mg
title: CIL:7331, Opercularia [NCBITaxon:168247], Opercularia coarctata, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

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; unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: High resolution of the layer of contractile myonemes in Opercularia coarctata that covers most of the cytosolic side of the pellicle. Pellicular pores (the clathrin coated pits of ciliates) penetrate through this sheet. The ER is spread out against this sheet and, besides having decorated tubules, it bears thinner rails that lie between the ER and the myonemes and spindle-shaped mid pieces. For a description of these rails and mid pieces as they are found in peritrichs. Their function still remains to be determined. TEM taken on 6/7/69 by R. Allen with Philips 300 operating at 60kV. Neg. 14,800X. The raw film was scanned with an Epson Perfection V750 Pro. this image is suitable for quantitative analysis.

Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness.

Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0736pnq
title: CIL:13440, Saccharomyces cerevisiae S288c. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: constrained iterative deconvolution
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
description: Intracellular localization of GFP-Vps74 in a wild-type S. cerevisiae background grown at 37C. In wild-type cells incubated at 26C or 37C, GFP-Vps74 is localized to Golgi compartments and the cytosol. The Golgi-localized PtdIns 4-kinase in yeast is composed of the Pik1 catalytic subunit and a myristoylated calcium-binding protein, Frq1. Vps74 is essential to maintain glycosyltransferases in the Golgi and results in this study reveal a previously unrecognized PtdIns4P-binding site in Vps74/GOLPH3 family proteins and link Pik1 signaling to retention of Golgi-resident proteins. 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 Fig1A Vps74/wild-type 37C panel in J Cell Biol. 187: 967-975. 2009. Images in Fig 1A include CIL#s 13439, 13440, 13441, 13442, 13443, 13444, 13445, 13446, 13447, 13448, 13458, 13459.
DOI: 10.6075/j0ht2nx3
title: CIL: 52969, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Image 4, z=20 from SC_011
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 image
DOI: 10.6075/j0445m46
title: CIL: 54458, Homo sapiens. In Cell Image Library

description: Imaging mode: bright-field microscopy
Visualization methods: 4G8 IHC using HRP/DAB
description: 5 um sections of FFPE prefrontal cortex tissue from post-mortem, human Alzheimer's disease donor labeled for amyloid-beta (4G8).
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.
DOI: 10.24339/d86636f1-e0ab-40d9-98b8-2592fdab6ad4
title: Experiences of gender regulation, focusing on developmental and gendered discourses

description: This dataset is from individual interviews with 10 nonbinary youth aged between 16-21 years old, living in the U.K. The research focused on the experiences of gender regulation, focusing on developmental and gendered discourses. The data includes a sample from the discursive realms and 1 poem.
DOI: 10.57903/uj/7l4rxm
title: Motion Energy Analysis (MEA) - software data
title: Motion Energy Analysis (MEA) - dane oprogramowania

description: Dane pozyskane w ramach projektu badawczego „W jednym rytmie. Style przywiązania a synchronizacja fizjologiczna i behawioralna uczestników grupowego treningu psychologicznego prowadzonego stacjonarnie i online”. Projekt badawczy został sfinansowany ze środków Narodowego Centrum Nauki (2022/06/X/HS6/00621). W ramach badań zebrano nagrania wideo uczestników spotkania grupowego z psychologiem. Następnie nagrania zostały przeanalizowane za pomocą oprogramowania MEA - celem wykrycia możliwej synchronizacji behawioralnej pomiędzy uczestnikami badania, rozumianej jako współwystępowanie ruchu (głowy)
description: Data obtained as part of the research project "In one rhythm. Attachment styles and physiological and behavioral synchronization of participants attend in group psychological training conducted face to face and online". The research project was financed by the National Science Center (2022/06/X/HS6/00621). As part of the research, video recordings of participants of a group meeting with a psychologist were collected. Then the recordings were analyzed using MEA software - to detect possible behavioral synchronization between study participants, understood as the co-occurrence of movement (head movement)
DOI: 10.6075/j0c827vg
title: CIL:47551, Staphylococcus aureus, neutrophil, endothelial cell. In Cell Image Library

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: 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: Visualization of neutrophil recruitment in capillaries proximal to agarose beads. (Figure 3 - Mac1)
DOI: 10.6075/j0j67g38
title: CIL:14676, Oscillatoria tenuis. In Cell Image Library

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.
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