cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0vx0fv3
title: CIL:45845, Homo sapiens. In Cell Image Library

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.
description: Plate 25426 - 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.
DOI: 10.6075/j03t9fvn
title: CIL:38708, Chlamydomonas reinhardtii. In Cell Image Library

description: Cells were fixed with glutaraldehyde, post fixed with osmium tetroxide, dehydrated, embedded in epoxy resin, and thin sections cut, stained and examined with a Hitachi HU-11C TEM.
description: Cells of the unicellular photosynthetic alga Chlamydomonas reinhardtii were fixed, sectioned, and examined by transmission electron microscopy. In this section of the ac-5 mutant grown phototropically, stacks (S) are primarily composed of two thylakoids. See Fig 10 in Goodenough and Staehelin 1971 J Cell Biol 48:595-619.
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)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide; uranyl salt; lead salt
Data qualification: Processed
DOI: 10.5281/zenodo.17459967
title: Data for "Should elephants graze or browse? The nutritional and functional consequences of dietary variation in a mixed-feeding megaherbivore"

description: Supplementary files used in the paper:

Gautam H, Berzaghi F, M. T, Ravichandran A, Sreeman SM, Sankaran M. 2025. Should elephants graze or browse? The nutritional and functional consequences of dietary variation in a mixed-feeding megaherbivore. R. Soc. Open Sci. 12: 250939. https://doi.org/10.1098/rsos.250939
DOI: 10.5281/zenodo.17459968
title: Data for "Should elephants graze or browse? The nutritional and functional consequences of dietary variation in a mixed-feeding megaherbivore"

description: Supplementary files used in the paper:

Gautam H, Berzaghi F, M. T, Ravichandran A, Sreeman SM, Sankaran M. 2025. Should elephants graze or browse? The nutritional and functional consequences of dietary variation in a mixed-feeding megaherbivore. R. Soc. Open Sci. 12: 250939. https://doi.org/10.1098/rsos.250939
DOI: 10.6075/j0qc02gv
title: CIL:36739, Paramecium multimicronucleatum, 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; Print from negative scanned for Photoshop.
Data qualification: Processed
description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Secondary lysosomes dock only with phagoacidosome membrane at a distance of 40nm. As during acidosome fusion with phagosomes, fusion of the many lysosomes with the phagoacidosome occurs at nearly the same time. Some small vesicles can be found close to the lysosomal surface. Such small vesicles might represent primary lysosomes originating from Golgi complexes, such as the coated vesicle in the upper left corner of this micrograph might suggest. TEM taken on 8/16/80 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 31,500X. Bar = 0.2µm.
DOI: 10.6075/j0kw5dw6
title: CIL:26569, Mus musculus, embryonic stem cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD)
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; differences in adsorption or binding of stain
Visualization methods: 4',6-diamidino-2-phenylindole (DAPI); EGFP
Processing history: constrained iterative deconvolution
Data qualification: Processed;spatialmeasurements
description: Z-series image of mouse ES cells carrying an alpha-globin BAC transgene array (clone 7d) transduced with a lentivirus containing an expression cassette for EGFP-LacI. EGFP-LacI binding (green) to the 256mer lac operator repeat contained within the BAC identifies the location of the BAC transgene array relative to the nuclear periphery, highlighted by anti-nuclear pore immunostaining (red), and nuclear interior, revealed by DAPI staining (blue). In contrast to the peripheral localization of beta-globin BAC transgene arrays, the alpha-globin BAC transgene arrays do not show the same bias towards the periphery.
description: Formaldehyde fixed cells were imaged using an IMT-2 Olympus fluorescence microscope with 60x 1.4 NA objective lens. Z-series were recorded, and the slices processed by iterative constrained deconvolution. 
See also: P Sinclair et al. 2010 Dynamic plasticity of large scale chromatin structure revealed by self-assembly of engineered chromosome regions. J Cell Biol 109:761-776.
DOI: 10.6075/j0tb161n
title: CIL:12308, Nassula, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: The top of the cytopharyngeal basket showing a closed cytostome where food will be engulfed. In the lab Nassula was fed Phormidium inundatum, a cyanobacterium. Ingested food is seen in food vacuoles as intensely stained blobs which are in various stages of digestion. TEM taken on 4/1/69 by R. Allen with Philips 300 operating at 60kV. Neg. 4,270X. Bar = 1µm.
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; Print from negative scanned for Photoshop
Data qualification: Processed;spatialmeasurements
description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm. A print of the negative was scanned and processed in Photoshop. This image is best used for qualitative analysis. There is a high resolution version of this image in the library (CIL:39137) which is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j05q4vzn
title: CIL:37057, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: This is IMAGE #1 (0 hours) of a neuron from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47. 
 
 Complete z-stacks were acquired of this neuron at a 2 hour interval over 8 hours. These images are part of this image group. This time lapse series shows the development of the neuron's dendritic arbor. The dendritic arbor exhibits morphological plasticity with branch additions, retractions and extensions.
 
 The cell was transfected with in vivo electroporation of plasmid DNA encoding eGFP ~24 hours before the 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: EGFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j05x2828
title: CIL:10512, Toxoplasma gondii RH. In Cell Image Library

description: A monolayer of human foreskin fibroblast cells was infected with Toxoplasma gondii expressing EGFP-tagged TgCentrin2 and mCherry-tagged TgIMC1 (innermembrane complex scaffold protein). Images acquired using API DeltaVision on a Olympus IX70 inverted microscope. Objective: Olympus 100X oil immersion, 1.35 NA. Filters: EGFP, ex 450-490 em 500-540, mCherry, ex 555-592 em 600-665. Dichromatic mirror: Chroma 89021. Captured with CoolSnapHQ/ICX285. Data stack corresponds to CIL# 10511.
Unpublished image that is similar to images published in PMID: 16518471. See publication for other experimental details.
description: Preparation: living tissue
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; mCherryFP
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0057fr2
title: CIL:37040, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

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: EGFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
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: This is IMAGE #1 (0 hour) of a time lapse series contained with in this image group. It shows neurons from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47.
 The pigment cells in the skin have high autofluorescence and are visible in the superficial layers of the z-stack.
 
 The images were acquired at 4 hour intervals over 8 hours, and show morphological plasticity of the dendritic arbor with branch additions and retractions.
 
 These cells were transfected with in vivo electroporation of plasmid DNA encoding eGFP ~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.
DOI: 10.6075/j0df6rbh
title: CIL:40071, Rattus norvegicus, astrocyte, astrocyte of the hippocampus. In Cell Image Library

description: Intracellular injection of astrocytes in lightly fixed tissue slices was performed as previously described, with some modifications (Buhl et al., [1990], PMID: 2262598). The brain was placed in ice-cold PBS and cut into coronal slices with a vibratome at a thickness of 100 µm, and stored in PBS at 4°C until used. The slices were placed under a 60x water objective (NA 1.4) and observed with an Olympus BX50WI microscope using infrared-DIC optics (Olympus, Melville, NY). Astrocytes in the upper blade of the dentate gyrus were identified by the shape and size of their somata. Glass micropipettes (OD 1.00 mm, ID 0.58 mm; resistances 100-400 M) were pulled on a vertical puller (David Kopf Instruments, Tujunga, CA) and backfilled with either 5% aqueous LY in 200 mM KCl. Astrocytes were impaled and iontophoretically injected with dye using 1-second pulses of negative current (0.5 Hz) for 1-2 minutes. After several cells were filled, the slices were placed in ice-cold 4% PFA for at least 1 hour. The slices were then ready to be immunolabeled. The rabbit anti-EphA4 antibody was provided by Dr. Elena Pasquale (The Burnham Institute, La Jolla, CA). EphA4 was subsequently detected using goat anti-rabbit Cy5. Slices were coverslipped using Gelvatol (Harlow and Lane, [1988]) and allowed to set overnight at room temperature before they were examined.
Image acquisition and analysis: Specimens were examined using a Radiance2000 laser scanning confocal system (Bio-Rad, Hercules, CA) attached to a Nikon E600FN microscope (Kanagawa, Japan). A 60x oil immersion (NA 1.4) objective was used to image LY-filled astrocytes.
description: Projection through merged optical section series of a filled astrocyte (green) in the molecular layer of the dentate gyrus of a 1 month-old rat, stained for EphA4 (red), showing the relationship between astrocyte processes and laminar boundaries revealed by EphA4 staining. Optical sections were generated with a single photon confocal microscope. Original data contributed to Bushong EA, Martone ME, Ellisman MH. Examination of the relationship between astrocyte morphology and laminar boundaries in the molecular layer of adult dentate gyrus. J Comp Neurol. 2003 Jul 21;462(2):241-51. PMID: 12794746. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
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; distribution of epitope
Visualization methods: lucifer yellow; primary antibody plus labeled secondary antibody; Cy5
Data qualification: Processed
DOI: 10.6075/j0p849hc
title: CIL:48827, Mus musculus, MC57-Cerulean. In Cell Image Library

description: Item type: confocal microscopy
description: To determine the origin (local vs. circulating) of tumor associated fibroblasts, a parabiotic pair of mice was created where only one mouse expressed EGFP under the control of the type I collagen alpha-1 promoter (COL-EGFP), and the other mouse expressed DsRed ubiquitously. On each mouse of the parabiotic pair, MC57-Cerulean cancer cells were injected on the distal flank. This folder contains images from the tumor grown in the DsRed mouse, freshly explanted and analyzed ex vivo. The blue channel shows cancer cells, the red channel shows DsRed cells, the green channel shows COL-EGFP+ fibroblasts (absent in the DsRed mouse tumor). Image name: 120513 parab dsred tumor flank.lif - 3 

Project: 20389
description: Mice were euthanized and tumors were freshly explanted. 1-2 mm thick sections were cut at different depths and kept in PBS during the imaging session. Fluorescent confocal microscopy was done using a Leica SP5 II TCS tandem scanner 2-photon spectral confocal microscope with XY motorized stage, using a 25X/NA 0.95 water lens from Leica.
DOI: 10.6075/j0xw4hmk
title: CIL:11204, Siphonaptera, unclassified Insecta, epithelial cell. In Cell Image Library

description: Freeze-fracture preparation of a continuous junction on the lateral surface of epithelial cells from the gut of a flea. Meandering ridges appear to be on the P-face of the replica. Figure 80, by Susumo Ito, 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.
description: Preparation: freeze_fracture/freeze_etch
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
DOI: 10.6075/j0833qv0
title: CIL:11209, Phodopus, Ambystoma, squamous 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
Visualization methods: osmium tetroxide
Data qualification: Processed
description: Upper panel, adjoining portions of two cells in the stratum spinosum of hamster cheek pouch epithelium shows desmosome junctions between two cells. Lower, a portion of the basal surface of a cell in the epidermis of a larval salamander Ambystoma punctatum shows hemi-desmosomes spaced at regular intervals. Figures 83 (upper, by J.T. Albright and M.A. Listgarten) and 84 (lower, by E. Hay) 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/j0b27t2q
title: CIL:11206, Periplaneta americana, epithelial cell. In Cell Image Library

description: Preparation: freeze_fracture/freeze_etch
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: reprinted with permission as Figure X 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.
description: Figures 81 (upper) and 82 (lower) from Chapter 3 (Junctional Specializations) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. Septate junctions (upper, rectum; lower, testis) in the cockroach Periplaneta americana appear as rows of 6-10nm particles on the P-face and shallow pits on the E-face of freeze fracture replicas. Images by Nancy Lane. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
DOI: 10.6075/j0jh3k0r
title: CIL:11215, Mus musculus, non-pigmented ciliary epithelial cell, epidermal cell. In Cell Image Library

description: Images of desmosomes from conventional EM and freeze fracture preparations show transmembrane filaments that link two hemidesmosomes. Upper: section of a cell boundary in the ciliary epithelium of the eye; middle, cross fracture across the boundary between two ciliary epithelial cells; lower, replica of a portion of the plasma membrane of an epidermal cell from newborn mouse. Figures 90 (upper), 91 (middle) both courtesy of Giuseppina Raviola, and 92 (lower, from Peter Elias and Daniel Friend) 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.
description: Preparation: crosslinking-fixative fixed tissue; tissue in plastic embedment; freeze_fracture/freeze_etch
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; differences in deposition of metal shadow
Visualization methods: osmium tetroxide; shadowing and plating
Data qualification: Processed