cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j07944rr
title: CIL:36308, Rattus, astrocyte. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: vibratome-sectioned tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: intracellular filling
Visualization methods: lucifer yellow
Data qualification: Processed
description: Male Sprague Dawley rats, 3 weeks of age, were anaesthetized and perfused transcardially with with Ringer's solution (37°C), followed by 4% paraformaldehyde (PFA) in PBS (37°C, pH 7.4). Tissue was sectioned (100 µm thick) using a vibratome, and injected with a BX50WI microscope (Olympus, Melville, NY) and, using infrared differential interference contrast videomicroscopy,cells with a small diameter soma (approx. 7–11µm) in the stratum
radiatum of CA1 were located and impaled with glass micropipettes filled with 5% aq. Lucifer Yellow. The astrocytes were filled using a 0.5 Hz pulses of current until all of the processes were brightly fluorescent. After several astrocytes were filled, a slice was placed in the 4% PFA overnight at 4°C. Slices were then imaged after coverslipping in Gelvatol. Confocal images were acquired with a BioRad Radiance2000 (Hercules, CA) attached to a Nikon E600FN (Kanagawa, Japan) microscope equipped with a Nikon (Tokyo, Japan) 60x oil objective (NA 1.4). Additional details are provided in Bushong EA, Martone ME, Ellisman MH. Maturation of astrocyte morphology and the establishment of astrocyte domains during postnatal hippocampal development. Int J Dev Neurosci. 2004 Apr;22(2):73-86.
description: Intracellular dye injections of protoplasmic astrocytes from the CA1 region of hippocampus of 3 week old rat reveals highly ramified spongiform processes that span territories with minimal overlap. Astrocytes were filled with Lucifer Yellow. Optical sections were generated with a single photon confocal microscope, and compiled to produce this maximum intensity projection image.
DOI: 10.6075/j0zc8251
title: CIL:38862, Didinium nasutum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: A high resolution view of a dividing Didinium nasutum. This large ciliate is capable of engulfing Paramecium. It has a thick ectoplasm containing numerous mucocysts embedded in its extensive epiplasm. It's external surface is coated with a layer of bacteria in this dividing cell. The cytoplasm is relatively compact under the conditions of fixation used. Electron opaque vacuoles are scattered in the cytoplasm. (For a more detailed report see Wessenberg and Antipa, Protistologica 4:427-447, 1968). TEM taken on 5/9/69 by M. Sage with Philips 300 operating at 60kV. Neg. 3,120X.
description: This digitized image is available 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/).
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
DOI: 10.6075/j0h1311f
title: CIL:7324, Escherichia coli, prokaryotic cell. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: living tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label; distribution of a specific protein
Visualization methods: DsRed-ExpressFP; Alexa Fluor 488; macromolecular probe
Processing history: unprocessed raw data
description: This is one of four related images of F-pili (conjugative pili encoded by the F plasmid of E. coli) dynamics by live-cell imaging. There are 2 movie (.avi) files and 2 files (.tiff) from the movies. The movies show that F-pili normally undergo cycles of extension and retraction in the absence of any obvious triggering event such as contact with a recipient cell.

Retraction of an F-pilus. E. coli strain HfrH expressing the red fluorescent marker DsRed Express were mixed with R17 bacteriophage labeled with Alexa 488 (green); R17 bacteriophage (NCBITaxon:12026) bind to the sides of F-pili. 

Samples were imaged by using a Zeiss LSM 510 confocal microscope with a Plan-Apochromat 63 × 1.4 N.A. DIC objective. Alexa-488 was excited with the 488-nm line of an argon laser with a 505–530-nm filter for emission, and DsRed was excited with the 543-nm line of a HeNe laser, with a 560-nm long pass filter for emission. An HFT UV/488/543 beam splitter was used. Images were collected in a single focal plane at 2 s intervals and accompanying movies (.avi) are playing at 10fps.
DOI: 10.6075/j0rr1xw2
title: CIL: 54431, Homo sapiens, astrocyte. 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: GFAP IHC using HRP/DAB
description: 5 um sections of FFPE prefrontal cortex tissue from post-mortem, human non-symptomatic donor labeled for glial fibrillary acidic protein (GFAP), a protein commonly used to identify astrocytes.
DOI: 10.6075/j00c4twb
title: CIL:9926, notopthalmus viridescens, erythrocyte. In Cell Image Library

description: Newt (Notopthalmus viridenscens erythrocytes were isolated in 0.1M KCl, spread on the surface of Na-citrate, picked up on formvar-carbon films, fixed with glutaraldehyde,stained with uranyl acetate and critical point dried. Images were recorded at 10KX and accelerating voltage of 1MeV at the University of Wisconsin HVEM facility.This image was taken with a specimen tilt of 60 degrees. A grouped image of the same field at a 50 degree tilt provides an oblique stereo view of tangled chromatin fibers emanating from the dispersed nucleus.
description: Preparation: glutaraldehyde fixed tissue; critical_point dried specimen
Relation to intact cell: spread nucleus
Item type: film
Imaging mode: transmission electron microscopy (TEM); illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: visualization of contiguous regions; uranyl salt; positive stain
Processing history: unprocessed raw data
DOI: 10.6075/j0n879h6
title: CIL: 54103, Homo sapiens, HeLa. In Cell Image Library

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: TK 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: Visualization methods: confocal microscopy
DOI: 10.6075/j0n58kp3
title: CIL:40682, Mus musculus, fibroblast. In Cell Image Library

description: High voltage (1MeV) transmission electron microscopy image of an isolated metaphase chromatid pair from a mouse A9 cultured cell, showing the fiber-like structure and several pieces of attached membrane. The image was taken with a specimen tilt of 53 degrees. Grouped with it is an image with a tilt of 46 degrees, providing a pair that affords an oblique stereo view of the chromosome.
description: Preparation: glutaraldehyde fixed tissue; critical_point dried specimen
Relation to intact cell: isolated subcellular component
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Chromosomes were isolated from mouse A9 cells arrested in metaphase using a non-aqueous protocol, placed on a grid, and stained with uranyl acetate.
See also:
H. Ris 1981 Steroscopic electron microscopy of chromosomes. Meth Cell Biol 22:77-96
H. Ris 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:220-246.
DOI: 10.6075/j0sf2v3h
title: CIL:35383, Homo sapiens, cevical carcinoma. In Cell Image Library

description: Whole human female metaphase chromosome from metaphase arrested cell swollen in hypotonic medium and treated to remove histones. The resulting residual chromosome 'scaffold' was imaged at 1 MeV. This image was taken with a specimen tilt of 55 degrees. Grouped with it is an image of the same area at 45 degrees tilt, providing an oblique stereo view of the chromosome.
description: HeLa cells were metaphase-arrested by a 3hr treatment with colcemid, the cells mechanically broken by passage through a 22-gauge needle, exposed to hypotonic 75 mM KCl for 10 min. Samples were fixed with 3:1 methanol:acetic, treated to remove histones, spread on a water surface, picked up on formvar coated grids, critical point dried, and imaged with the Wisconsin HVEM at 1 MeV. See Ris (1978) Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:229-246; Ris (1981) Stereoscopic microscopy of chromosomes. Meth Cell Biol 22:77-96.
description: Preparation: coagulating-fixative fixed tissue; critical_point dried specimen
Relation to intact cell: whole mounted tissue
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
DOI: 10.6075/j0k35tb2
title: CIL: 53972, Homo sapiens, HeLa. In Cell Image Library

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
description: STE 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.
DOI: 10.5281/zenodo.15412641
title: Specimmune
DOI: 10.5281/zenodo.17492134
title: Specimmune
DOI: 10.6075/j02v2dqt
title: CIL:46279, Homo sapiens. In Cell Image Library

description: Plate 25943 - Phenotypic profiling attempts to summarize multiparametric, feature-based analysis of cellular phenotypes of each sample so that similarities between profiles reflect similarities between samples. This image set provides a basis for testing image-based profiling methods wrt. to their ability to distinguish the effects of small molecules.
 
Images
The images are of U2OS cells treated with each of 1600 known bioactive compounds and labeled with six labels that characterize seven organelles (the .cell-painting. assay).
 
This pilot experiment consists of 20 plates. Each plate has 384 wells and each well has 9 fields of view for a total of 69,120 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale image file, so there are 345,600 image files in 16-bit TIFF format.
description: Gustafsdottir et al. (doi:10.1371/journal.pone.0080999) have developed a multiplex cytological profiling assay that "paints the cell" with as many fluorescent markers as possible without compromising our ability to extract rich, quantitative profiles in high throughput. The assay detects seven major cellular components. In a pilot screen of bioactive compounds, the assay detected a range of cellular phenotypes and it clustered compounds with similar annotated protein targets or chemical structure based on cytological profiles. The results demonstrate that the assay captures subtle patterns in the combination of morphological labels, thereby detecting the effects of chemical compounds even though their targets are not stained directly. This image-based assay provides an unbiased approach to characterize compound- and disease-associated cell states to support future probe discovery.

Using the cell-painting assay, the Broad Institute has assembled a reference dataset of profiles for U2OS osteosarcoma cells treated with ~30,000 compounds. The compound collection includes DOS-derived compounds (20,000), as well as chemically diverse MLI compounds with biologically diverse performance identified through analysis of PubChem (10,000), and known bioactive compounds to serve as landmarks (2,500). The DOS compounds consist of structurally diverse and stereochemically rich compounds with structures distinct from the current MLSMR. The compound collection also includes 267 distinct compounds nominated by MLPCN Centers from projects for which the Centers would like to identify new chemical series with similar activities.

The experiment consists of 413 microtiter plates. Each plate has 384 wells. Each well has 9 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale 16-bit TIFF image file.
DOI: 10.6075/j0h994r4
title: CIL: 52501, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given tile position
description: Tile x=5, y=2, z=14 from BL32077_Myc_Terc
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
DOI: 10.6075/j0gh9hk6
title: CIL: 53313, Drosophila melanogaster, Entire Organism. In Cell Image Library

description: Video of fruit fly embryonic development. Video filename format is as follows organism_temperature_embryo. Data was collected at 27 degrees Celcius
description: Imaging mode: Gray Scale
Visualization methods: 20x magnification captured by one of the following eyepiece cameras: Swiftcam 3 Megapixel, OMAX 9.0 MP, AmScope MU300
description: 27 degrees ℃
DOI: 10.6075/j06w98x3
title: CIL:11232, non-pigmented ciliary epithelial cell. In Cell Image Library

description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Data qualification: Processed
description: Gap junctions in ciliary epithelium under conditions of oxygenation (upper) and anoxia (lower), in tissue prepared by ultrarapid freezing using liquid helium. Under oxygenated conditions, the connexons are spaced apart, and show no ordered arrangement. Under anoxia, the gap junction has hexagonally packed connexons. Images by Elio Raviola appear as Figures 100 (upper) and 101 (lower) from Chapter 3 (Junctional Specializations) 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.
DOI: 10.6075/j0zc824k
title: CIL:573, Acetabularia mediterranea, gamete. In Cell Image Library

description: At cyst formation in the 'giant' unicellular green alga Acetabularia, each cyst contains a single nucleus which subsequently undergoes several rounds of mitosis prior to gamete formation. Initially the nuclei form a syncytium which separates into individual gametes. This section shows a stage in gametogenesis where the syncytium is being divided into uninuclear gametes, and the formation of flagella from paired centrioles is in progress. See Woodcock and Miller, 1973. Ultrastructural features of the life cycle of Acetabularia I Gametogenesis. Proptoplasma 77, 313-319.
description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); illumination by electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; osmium tetroxide; lead salt
Processing history: unprocessed raw data
description: Cysts were fixed in glutaraldehyde, post-fixed in osmium tetroxide, epoxy embedded, and thin sections stained with aqueous uranyl acetate and lead citrate. Grids were examined with a Philips 400 TEM operated at 80KV and images recorded on film.
DOI: 10.6075/j0125rxj
title: CIL:723, Chlorocebus sabaeus. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: living tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: UV/visible/IR photons
Visualization methods: EGFP
description: COS 7 cell expressing Organelle LightsTM ER-GFP (Invitrogen) consiting of the signal sequence of the ER protein calreticulin and a KDEL
retention sequence. Images were collected with a 63X 1.4 NA Plan-Apochromat oil objective on a Zeiss LSM510 META (Carl Zeiss,Thornwood, NY) using 488 nm excitation, HFT 488 dichroic, and LP505 emission filter. Image size is 1024 x 1024, pixel size is 0.07 µm x 0.07 µm and pixel time was set to 1.28 ¬µsec. Detector pinhole was set to collect 100 ~0.5 µm slices at ~4 sec intervals.
DOI: 10.6075/j0rv0njx
title: CIL:36996, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: This is IMAGE #2 (day 2) of a time lapse series contained with in this image group. It is a neuron from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47. A second faint neuron is also visible.
 
 The images were acquired daily over 3 days and show dendritic arbor development and morphological plasticity of the dendritic arbor with branch additions and retractions.
 
 The cell was transfected with in vivo electroporation of plasmid DNA encoding eYFP ~24 hours before the first image was acquired. The intact, living tadpole was anesthetized, positioned under a glass coverslip and this image was taken directly through its transparent skin using a custom built two-photon microscope.
description: Specifications of the custom built two-photon microscope, including the laser sources, signal amplification, PMT specifications, and YFP filter sets are described in: 
Ruthazer ES, Li J, Cline HT. 2006. Stabilization of axon branch dynamics by synaptic maturation. J Neurosci 26(13):3594-3603. 

The methods of cell transfection with electroporation can be found here: 
Bestman JE, Ewald RC, Chiu S-L, Cline HT. 2006. In vivo single-cell electroporation for transfer of DNA and macromolecules. Nat Protocols 1(3):1267-1272. 

Further explanation can be found here:
Bestman JE, Cline HT. 2008. The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo. Proc Natl Acad Sci U S A 105(51):20494-20499.

Bestman JE, Cline HT. 2009. The Relationship between Dendritic Branch Dynamics and CPEB-Labeled RNP Granules Captured in Vivo. Front Neural Circuits 3:10.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EYFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0rb74fv
title: CIL: 54604, Mus musculus, RAW2647. In Cell Image Library

description: Processed data
description: Imaging mode: Lattice Light Sheet Microscope
Visualization methods: ChimeraX
description: Membrane Structure Comparison
DOI: 10.6075/j0w37wfs
title: CIL:39947, Rattus norvegicus, basket cell. In Cell Image Library

description: Maximum intensity projection of an optical section series of a basket cell from the rat cerebellar vermis. This cell was labeled by intracellular injection of lucifer yellow, and imaged using Biorad MRC 1024 confocal with a 40X, NA 1.4 objective. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
description: Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Visualization methods: intracellular filling; lucifer yellow
Data qualification: Processed