cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0tm7b37
title: CIL:3042, Rattus, multipolar neuron. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
description: Development of the axon and dendritic arbors in cultured hippocampal neurons after 7 days in vitro. MAP2 staining (red) highlights the dendrites, while microtubule staining (green) reveals both the axons and dendrites in the field of view. Neurons at 2, 3, 5 and 7 days in vitro are represented in this image group. 

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 tubulin (monoclonal DM1A, from Sigma with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and MAP2 (polyclonal Ab266, from S. Halpain with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 20X (Fluotar, NA 0.5) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. Image generated with the MetaMorph color combine function.
DOI: 10.6075/j0g44ps8
title: CIL: 52136, Homo sapiens. In Cell Image Library

description: A single molecule TIRFM assay was employed to measure the kinase activity of purified PI3K molecules on a supported lipid bilayer by counting the number of product PIP3 molecules they produce.
description: Imaging mode: Fluoresence
Visualization methods: objective based TIRFM using a modified Nikon TE-2000U (60x 1.49 N.A. TIRF objective) and illumination from a 532-nm solid-state laser with power modification by neutral-density filters
description: This assay utilizes physiological concentrations class I PI3Ka, 1mM ATP, drug identified in subfolder, and saturating concentrations of fluorescently-labeled GRP-PH domain, a PIP3 product lipid binder, in order to count each product lipid produced. Enzyme rates are calculated as the slope of product lipid created vs. time. 21.5 ± 0.5°C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
DOI: 10.6075/j0vt1qph
title: CIL:46304, Homo sapiens. In Cell Image Library

description: Plate 24562 - 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: 10.15468/dl.k7gfpv
title: Occurrence Download

description: A dataset containing 2427 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "OccurrenceStatus is Present",
 "TaxonKey is Crax alberti"
 ]
}

 The dataset includes 2427 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009307-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fnq83v
title: Occurrence Download

description: A dataset containing 8484 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is India",
 "GadmGid is one of (IND.13_1, IND.35_1, IND.30_1, IND.4_1, IND.3_1, IND.22_1, IND.33_1, IND.23_1, IND.21_1, IND.36.6_1, IND.24_1, Z01.14.13_1)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Mammalia"
 ]
}

 The dataset includes 8484 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009306-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0q23zzx
title: CIL: 54116. 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: 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.
DOI: 10.6075/j0pc32h4
title: CIL:40189, Homo sapiens, pyramidal cell, neuron of cerebral cortex. In Cell Image Library

description: Single image from a serial section electron microscopic reconstruction of the cell body of a cortical pyramidal neuron from a biopsy sample obtained from the cortex of a patient with Alzheimer's disease. The specimen was prepared from biopsy material obtained several decades ago. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. For more information, see: Ellisman et al. Neuronal fibrillar cytoskeleton and endomembrane system organization in Alzheimers disease, In Alteration of the Neuronal Cytoskeleton in Aging and Dementia, GP Perry (Ed,).pp, 61-73, Plenum Publ, Corp, New York, 1988.
description: Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Data qualification: Processed
description: Single image from a serial section electron microscopic reconstruction of the cell body of a cortical pyramidal neuron from a biopsy sample obtained from the cortex of a patient with Alzheimer's disease. The specimen was prepared from biopsy material obtained several decades ago. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database. For more information, see: Ellisman et al. Neuronal fibrillar cytoskeleton and endomembrane system organization in Alzheimers disease, In Alteration of the Neuronal Cytoskeleton in Aging and Dementia, GP Perry (Ed,).pp, 61-73, Plenum Publ, Corp, New York, 1988.
DOI: 10.6075/j09g5kzj
title: CIL:12302, Didinium nasutum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Lamellae of cytopharynx in the opisthe of a dividing cell. This cytopharynx is not yet functional and lacks most of the medium dense vesicles that accumulate between the lamellae. Toxicysts are present. One toxicyst has myelin-like layers at the level it was sectioned. Bacteria align adjacent to the cell. they may be symbiotic. TEM taken on 5/9/69 by M. Sage with Philips 300 operating at 60kV. Neg. 9,250X. Bar = 1µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. A high resolution image is in the library (CIL:38864) and 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; Print from negative scanned to Photoshop.
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j0bk1btp
title: CIL: 51890, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: A novel cell population analysis to quantify both initial and long-term drug effects, namely pseudopod adaptation and recovery following an initial drug-induced perturbation, adding drug slowly in 1/4 increments over 90 minutes.
description: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
description: Imaging mode: DICM
Visualization methods: Spinning disc confocal DICM & widefield DICM Using a Nikon TiE microscope equipped with a 40x, 0.95 N.A. objective and a Hamamatsu ORCA-Flash 4.0 V3 Digital CMOS camera, or a Nikon TiE spinning-disc confocal microscope equipped with a Yokogawa CSU-X1 scanning unit, an Andor iXon 888 EMCCD camera, and a 60x, 1.3 N.A. water-immersion objective or a 40x, 0.95 N.A. objective
DOI: 10.6075/j0r49ph2
title: CIL:12294, Homo sapiens, epithelial cell. In Cell Image Library

description: MCF-10Aeco cells were seeded on coverslips at a low density. At 3 h after seeding cells were fixed and immunostained for tubulin (Cy2, 488 nm laser), EB1 (rhodamine red-X, 543 nm laser) and LL5s (Cy5, 633 nm laser), and observed using a LSM510 confocal laser-scanning microscope system.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: Cy2; Cy5; X-Rhodamine
Data qualification: Raw
description: Localization of the microtubule anchoring factor LL5α (red), microtubules (green), and the microtubule plus-end binding protein, EB1 (blue) in an MCF-10Aeco epithelial cell. EB1 was concentrated in regions of LL5 accumulation. Overall findings from this publication showed that signaling from laminin-integrin associations plays a role in attaching microtubule plus ends to the epithelial basal cell cortex. This image is the original data file for Fig. 1 C from J Cell Biol (2010) 189 (5):901-917.
DOI: 10.6075/j0416vpm
title: CIL:37141, Rattus, pancreatic acinar cell. In Cell Image Library

description: Preparation: chemically fixed tissue
Relation to intact cell: 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
Processing history: unprocessed raw data
description: Additional Reference:
Valentijn, K.M., F.D. Gumkowski and J.D. Jamieson. 1999. J. Cell Science. 112:81-96.

Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original magnification 33,000X.
description: Transmission electron micrograph of exocytosis taken from the rat pancreas. Images such as these indicated that secretory granules closely and selectively approach the apical membrane of the pancreatic acinar cell where exocytosis takes place, fuse with the apposed membrane, and release the content of secretory proteins into the acinar lumen without broaching the intracellular environment. The resulting omega figure is transitory, suggesting that the excess granule membrane is retrieved/recycled. Note the actin coat around the newly inserted granule membrane. Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
DOI: 10.6075/j0xd112n
title: CIL:41123, Enterobacteria phage T4, Escherichia coli. In Cell Image Library

description: Images collected on a JEOL 1010 TEM. Please refer to http://remf.dartmouth.edu:8080/EM-Wiki for details on specimen preparation.
description: Transmission electron microscope image of T4Phage on the surface of Escherichia coli bacteria. T4Phage is a bacteriophage that infects E. coli bacteria.
description: Preparation: whole mounted tissue
Relation to intact cell: whole mounted 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: uranyl salt
Processing history: unprocessed raw data
DOI: 10.5281/zenodo.17489582
title: pH-Sensitive Amino Lipid-Driven Pore Formation Enables Endosomal Escape of Lipid Nanoparticles

description: Dataset containing source data, all necessary files for coarse-grained molecular dynamics simulations for the "pH-Sensitive Amino Lipid-Driven Pore Formation Enables Endosomal Escape of Lipid Nanoparticles" research article
DOI: 10.5281/zenodo.17489583
title: pH-Sensitive Amino Lipid-Driven Pore Formation Enables Endosomal Escape of Lipid Nanoparticles

description: Dataset containing source data, all necessary files for coarse-grained molecular dynamics simulations for the "pH-Sensitive Amino Lipid-Driven Pore Formation Enables Endosomal Escape of Lipid Nanoparticles" research article
DOI: 10.6075/j06w99jk
title: CIL: 51889, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: Imaging mode: DICM
Visualization methods: Spinning disc confocal DICM & widefield DICM Using a Nikon TiE microscope equipped with a 40x, 0.95 N.A. objective and a Hamamatsu ORCA-Flash 4.0 V3 Digital CMOS camera, or a Nikon TiE spinning-disc confocal microscope equipped with a Yokogawa CSU-X1 scanning unit, an Andor iXon 888 EMCCD camera, and a 60x, 1.3 N.A. water-immersion objective or a 40x, 0.95 N.A. objective
description: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
description: A novel cell population analysis to quantify both initial and long-term drug effects, namely pseudopod adaptation and recovery following an initial drug-induced perturbation, adding drug slowly in 1/4 increments over 90 minutes.
DOI: 10.6075/j0c24wkf
title: CIL:40171, Rattus norvegicus, astrocyte, astrocyte of the hippocampus. 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; distribution of epitope
Visualization methods: Alexa Fluor 568; primary antibody plus labeled secondary antibody; lucifer yellow
Data qualification: Processed
description: Projection through merged optical section series of adjacent hippocampal astrocytes from a 1-week old male rat, injected with Lucifer Yellow (green) and Alexa568 (red) respectively, imaged with confocal microscopy. Optical sections were generated with a single photon confocal microscope. Original data contributed to 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. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
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 Alexa 568. 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 immunostained and 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 astrocytes.