cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j090235g
title: CIL: 50718, FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles: 5.6_Cell_5_Surface_Rendering. In Cell Image Library

description: FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles. Postnatal day 4 mouse Inner Ear Organ of Corti labeled with anti-PKHD1L1 antibody (10 nm gold beads). The dataset represents the apical end of the Outer Hair Cell with the stereocilium bundle. Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample.
description: Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample. 
5.6_Cell_5_Surface_Rendering is a compressed (zipped) folder containing all files required to render the surface of the bundle. Also included is the ‘ProjectLog’ file produced by Slice and View acquisition software.
This file is a part of Dataset 5, comprised of files related to the Cell #5 of current study. The numbering order of the files reflects the order of operations performed during the analysis.
description: Imaging mode: Serial Electron Microscopy; Focused Ion Beam Scanning Electron Microscopy (FIB-SEM)
Visualization methods: Heavy metal stain (Osmium Tetroxide, Potassium Ferrocyanide, Tannic Acid); Immunogold labeling with 10 nm gold beads
DOI: 10.6075/j0sj1jqh
title: CIL:10011, Didinium nasutum, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Didinium has two bands of ciliated basal bodies that encircle the cell, one adorally and one aborally. The bands are composed of groups of approximately 15 ciliated basal bodies. This section is a longitudinal section of the cilium and basal body and cross section of approximately seven different groups or pectinelles. The proximal end of basal bodies are ensheathed in electron opaque sleeves from which microtubular ribbons extend into the adjacent ridges on the two sides of each basal body. TEM taken on 5/20/69 by R. Allen with Philips 300 operating at 60kV. Neg. 14,800X.Bar = 0.5µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. A raw, unprocessed, high resolution version of this image (CIL:4664) is in the library and 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: film; Print from negative scanned for Photoshop.
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j07080sz
title: CIL:40120, Homo sapiens, HTLV-1 subtype A, mature CD4 single-positive thymocyte, T cell. In Cell Image Library

description: CD4+ T cells were isolated and cultured overnight to allow spontaneous expression of HTLV-1 proteins, and subsequently prepared for EM. To detect HTLV-1 Gag matrix protein in infected cells the samples were labelled against HTLV-1 Gag p19 (Tanaka et al., 1986) using the DAB kit from Molecular Probes (Invitrogen Ltd, Paisley, UK ). After the PFA/glutaraldehyde fixation, the samples were incubated in PBS containing 1% BSA, 0.1% Triton X-100 and 2% H2O2, for 1 h at 37uC to block non-specific antibody binding and to quench the endogenous peroxidase activity of the cells. To detect the HTLV-1 complexes, the cells were incubated with 5 mg/ml of anti-Gag p19 (GIN7 mAb) [33] diluted in PBS 1% BSA, for 1 h at 37uC. Then the second antibody, anti-Mouse mAb conjugated to HRP (Invitrogen Ltd, Paisley, UK ), was added at a final dilution of 1 mg/ml, and incubated for 30 minutes at 37uC. The cells were washed three times with PBS containing 1% BSA between each step. For detailed methods of the preparation, refer to the CCDB link provided.
description: Preparation: osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Data qualification: Processed
description: A single computed slice through a tomographic reconstruction of a virological synapse formed between naturally HTLV-1 infected CD4+ T cells and autologous uninfected CD4+ target cells. HTLV-1 particles in the synaptic cleft were identified by immunolabeling using anti-Gag p19 labeling and peroxidase-DAB detection. 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: Majorovits et al. (2008) Human T-Lymphotropic Virus-1 visualized at the virological synapse by electron tomography. PLoS ONE 3: e2251, doi:10.1371/journal.pone.0002251, PMID 18509526
DOI: 10.6075/j0hh6hvz
title: CIL:13863, Saccharomyces cerevisiae. In Cell Image Library

description: Cells (MATa tem1::KanMX ura3::eGFP-BFA1–TEM1::URA3 cdc15::CDC15-3HA), grown in rich media with glucose, were fixed for 15 min in 3.7% formaldehyde and 0.1 M potassium phosphate buffer, pH 6.4. Cells were then washed twice with 0.1 M potassium phosphate buffer, pH 6.4, and resuspended in 1.2 M sorbitol in 0.12 M K2HPO4/0.033 M citric acid, pH 5.9. Fixed cells were digested with 0.1 mg/ml zymolyase-100T (US Biological) and 1/10 volume of glusulase (PerkinElmer) at 30C for 15 min, washed once, and resuspended in 1.2 M sorbitol in 0.12 M K2HPO4/0.033 M citric acid, pH 5.9. Primary antibodies were anti-HA monoclonal antibody (HA.11; 1:500) and anti-tubulin (Abcam; 1:500). Secondary antibodies were: anti-mouse Cy3 (for HA) and anti-rat FITC (for tubulin). Cells were resuspended in DAPI (1 mg/ml). Imaging was performed at 25C using a Leica DM6000 microscope equipped with a 100x/1.40 NA oil immersion objective lens, A4, L5, and TX2 filters, and a digital CCD camera (DFC350, Leica). Pictures were processed with LAS AF (leica) and ImageJ software.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: widefield illumination; fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; compartmentalization of stain or label
Visualization methods: HA peptide tag; 4',6-diamidino-2-phenylindole (DAPI); primary antibody plus labeled secondary antibody; Cy3; Fluorescein (FITC)
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: In tem1Δ cells expressing a Bfa1-Tem1 fusion protein, Cdc15-3HA (red) loads prematurely onto spindle pole bodies during metaphase as determined by spindle morphology (tubulin, green) and nuclear morphology (DAPI, blue). The Bfa1-Tem1 fusion protein is constitutively and asymmetrically targeted to spindle pole bodies. Compare with control image CIL# 13864. Image is Fig 3C, bottom panels, in J Cell Biol. (2011) 192: 599-614. Images in Fig 3 include CIL# 13862, 13863, 13864, 13865, 13866, 13867.
DOI: 10.6075/j00k274r
title: CIL:46010, 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 26203 - 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: 10.15468/dl.a8rpmk
title: Occurrence Download

description: A dataset containing 278 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (China, Hong Kong)",
 "TaxonKey is Bauhinia blakeana"
 ]
}

 The dataset includes 278 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009390-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0qc03km
title: CIL:39596, Saccharomyces cerevisiae. In Cell Image Library

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.
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP-tagged WHI5. WHI5 is a repressor of G1 transcription that binds to SCB binding factor (SBF) at SCB target promoters in early G1; phosphorylation of Whi5p by the CDK, Cln3p/Cdc28p relieves repression and promoter binding by Whi5; periodically expressed in G1.These phase,gfp z-series images are part of an image group that ranges from CIL:39596-39600. 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
DOI: 10.6075/j028069b
title: CIL:13913, Homo sapiens, permanent cell line cell. In Cell Image Library

description: Human colon carcinoma HCT 116 cells were transfected with a GFP-LC3-encoding plasmid, cultured in complete medium for 24 h and enucleated to obtain cytoplasts. The cytoplasts were treated with 100 µM Spermidine for 4 h. Cytoplasts were still able to accumulate GFP-LC3 puncta in response to spermidine or resveratrol treatment, indicating that nuclei (and by extension transcription) are not required for short-term autophagy stimulation by these two agents. Nuclei were counterstained by Hoechst. Confocal fluorescent images were captured using a confocal fluorescence microscope (TCS SP2; Leica) fitted with an Apochromat 63× 1.3 NA immersion objective. Images were acquired with a camera (DFC 350 FX 1.8.0; Leica) using LAS AF software (Leica) and processed with Photoshop (CS2; Adobe) software. Specifically, picture processing involved cropping of representative areas and linear adjustments of contrast and brightness and was performed using Photoshop (with equal adjustment parameters for all pictures); no explicit γ correction was used. Image: Figure 8A, right panel, in Morselli et al. J Cell Biol 192: 615-629
description: Preparation: isolated subcellular component
Relation to intact cell: enucleated cell
Item type: recorded image; charge coupled device (CCD)
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; differences in adsorption or binding of stain
Visualization methods: EGFP; membrane-permeant probe; Hoechst
Processing history: brightness and contrast adjusted
Data qualification: Processed;intensitiesquantitation
DOI: 10.15468/dl.yggshw
title: Occurrence Download

description: A dataset listing the 377 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Indonesia",
 "TaxonKey is Asteroidea"
 ]
}

 The dataset's 377 records were derived from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009382-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14601055
title: dataset related to NDCI-mGMM method

description: The final maize maps and validation samples data of each study site for the paper "NDCI-mGMM: A novel and automated model for dynamic maize mapping during the growing season".
DOI: 10.5281/zenodo.17490861
title: dataset related to NDCI-mGMM method

description: The final maize maps and validation samples data of each study site for the paper "NDCI-mGMM: A novel and automated model for dynamic maize mapping during the growing season".
DOI: 10.6075/j047498x
title: CIL:45826, Homo sapiens. In Cell Image Library

description: Plate 24797 - 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/j0154gwf
title: CIL:37029, 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: This is IMAGE #8 (time point: 8 hour, rapid time lapse)of an image group. It shows a neuron from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47. 
 
 This is a projection of the lapse series captured in IMAGE 7. It shows the dendritic arbor of this neuron every 60 seconds for 10 minutes. Over time, the tadpole (and the neuron) drifts across the field. 
 
 
 In the series, z-stacks of this neuron were acquired at a 2 hour interval for 8 hours. Afterward, a second time lapse series was acquired at a 60 second interval for 10 minutes. This time series shows 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 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.
DOI: 10.6075/j0dn43z1
title: CIL:25898, uncultured scuticociliate, Conchophthirus curtus, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: A glancing view of the cortex of Conchophthirus reveals details of cortical structure. This includes the nature of the cell membrane and the alveolar membranes that reside immediately below the surface; fibrillar and microtubular structures that support this ciliated cell, and in the case of Conchophthirus, the cortical mitochondria that may represent a single mitochondrion that has finger-like extensions that lie immediately between the rows of basal bodies and are independent of more typical vesicular mitochondria that reside in the inner cytoplasm. The negative magnification is 19,000X. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 65nm thickness. For greater detail see:Antipa, G. A. 1971. Structural differentiation in the somatic cortex of a ciliated protozoan, Conchophthirus curtus Engelmann, 1862. Protistologica 7:47l-501.
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
DOI: 10.6075/j0rn37fp
title: CIL: 52916, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Image 11, z=9 from SC_007
description: One z layer of a z-stack at the given image
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