cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0pn9514
title: CIL:45701, Homo sapiens. In Cell Image Library

description: Plate 20585 - 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/j0sq8zr9
title: CIL:45501, Homo sapiens, pluripotent stem cell. In Cell Image Library

description: Preparation: chemically fixed tissue
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: 4',6-diamidino-2-phenylindole (DAPI); primary antibody plus labeled secondary antibody
description: Differentiated human induced pluripotent stem cells (iPSCs) following differentiation protocol. Cell nuclei were stained with DAPI (blue), nestin (red) and beta3-tubulin/Tuj1 (green). Note the fate decision of some stem cells towards neuronal differentiation (left side) whereas the second type of cells (right side) differentiated towards brain microvascular endothelial cells (right side).
DOI: 10.6075/j0cz379k
title: CIL:45355, Mus musculus, mammary adenocarcinoma. In Cell Image Library

description: DA3 cells expressing the fluorescent protein mCherry were grown to 90% confluence in wells of 2 cm diameter in DMEM supplemented with 10% heat-inactivated FCS (Gibco-BRL). A scratch was generated using a 200 µl tip, and the cells were incubated with 80 ng ml-1 Met-Hepatocyte Growth Factor/Scatter Factor (HGF/SF) and subjected to time lapse confocal laser scanning microscopy (CLSM-510, Zeiss, Germany) for approximately 26 hrs, with images taken at 14.5 min intervals. The acquired differential interference contrast (DIC) channel of the time-lapse sequence (shown here) was used for the multi-cellular analysis; the red fluorescence channel was not used here, and is not shown.

The analysis used local motion-estimation information to extract spatiotemporal measures for cell acceleration, stretching (strain rate), and directional migration. The coloured strips in the video were extracted from this analysis. These results are under review and a reference to full details will be given upon publication.
description: Upon treatment with HGF/SF, cells close to the wound edge begin to accelerate and stretch, deforming to elongated morphology, followed by enhanced directional migration. Green represent acceleration and stretching, purple represents increased directional migration, and light blue the overlapping regions of acceleration, stretching and directional migration.
description: Item type: time lapse microscopy
Imaging mode: differential interference contrast microscopy
Data qualification: Processed
DOI: 10.15468/dl.xrhjmm
title: Occurrence Download

description: A dataset containing 4935 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((115.65785 -33.3285,115.66792 -33.32783,115.67031 -33.32569,115.66088 -33.31421,115.67063 -33.30566,115.64698 -33.30406,115.63692 -33.31234,115.63788 -33.31621,115.64011 -33.31902,115.63868 -33.32235,115.6465 -33.32703,115.65785 -33.3285))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Year 1995-2025"
 ]
}

 The dataset includes 4935 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009680-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0pk0f1b
title: CIL:44151, Mus musculus, fibroblast. In Cell Image Library

description: Imaging was performed using a Leica TCS SP5-AOBS 5-channel confocal system equipped with multiline Argon diode 561 nm, HeNe 594 nm and HeNe 633 nm. Images were recorded with a 40x 1.4 NA oil immersion objective lens, and 5 micrometer z-spacing and processed using Imaris software (Bitplane). 
See also: Malide D, Metais J-Y, and Dunbar CE. (2012). Dynamic clonal analysis of murine hematopoietic stem and progenitor cells marked by 5 fluorescent proteins using confocal and multiphoton microscopy. Blood. Dec 20;120(26):e105-16.
description: The image shows a 3D-rendering (Imaris software) of a live confluent culture of NIH-3T3 cells obtained using confocal microscopy. The cells were co-transduced with 5 fluorescent proteins and with Lentiviral Gene Ontology (LeGO) vectors expressing Cerulean (blue), EGFP (green), Venus (yellow), tdTomato (magenta) or mCherry (red) fluorescent proteins to provide combinatorial colors for progeny tracking. Groups of nearby cells of the same color descended from same stem cells. 
This image is grouped with two others obtained using a similar imaging strategy. 
 
See also Malide et al. (2012) Dynamic clonal analysis of murine hematopoietic stem and progenitor cells marked by 5 fluorescent proteins using confocal and multiphoton microscopy. Blood. Dec 20;120(26):e105-16.
 
An image obtained in the same manner that obtained an Honorable Mention in the 2011 Olympus BioScapes Digital Imaging Competition may be viewed as CIL:41631.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label
Visualization methods: CeruleanFP; EGFP; VenusFP; tdTomatoFP; mCherryFP
Data qualification: Processed
DOI: 10.6075/j0t1530c
title: CIL:44101, Mus musculus, primary striatal neuron. In Cell Image Library

description: Shown is a confocal microscopy image of a living isolated mouse neuron stained for DNA (nucleus, blue)and mitochondria (mitotracker, red, and the synthetic antioxidant XJB-5-131 labeled with BIODIPY-labeled (green). The image is from experiments examining oxidative damage and mitochondrial dysfunction in relation to aging and age-related neurodegenerative diseases including Huntington's disease. See: Xun et al. 2012 Targeting of XJB-5-131 to mitochondria suppresses oxidative DNA damage and motor decline in a mouse model of Huntington's disease. Cell Biol. Rep. 2:1137-1142.
description: Cultures of living primary striatal neurons isolated from embryonic HD150Kl mice were stained for mitochondria using two fluorescent probes and imaged using a Zeiss LSM 710 confocal laser scanning confocal microscope. Probes were MitoTracker Deep Red excited at 633 nm and the antioxidant XJB-5-131 conjugated to BIODYP and excited at 488 nm. DNA was labeled with DAPI (blue). Images were acquired with Zen Zeiss) and analyzed with FIJI. 
For further details see Xun et al. 2012 Targeting of XJB-5-131 to mitochondria suppresses oxidative DNA damage and motor decline in a mouse model of Huntington's disease. Cell Biol. Rep. 2:1137-1142.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: probe for mitochondria; 4',6-diamidino-2-phenylindole (DAPI); BIODIPY
DOI: 10.6075/j0ng4qsp
title: CIL:43758, Homo sapiens, epithelial cell. In Cell Image Library

description: HeLa cells carrying the appropriate EGFP-labeled transgene were fixed in cold methanol, rehydrated, and treated with mouse antibody to alpha-tubulin and goat antibody to GFP followed by donkey-anti-mouse Alexa 594, donkey-anti-goat Alexa 488 and Hoechst 33342. Preparations were examined using a Zeiss Axioplan 2 widefield microscope with a 63x NA 1.4 objective lens. Images were recorded using a CCD camera (CS472-95, Hamamatsu). 
For further details see: Zaliga M et al. 2013 A genomic toolkit to investigate kinesin and myosin motor funtion in cells. Nat. Cell Biol. published online Feb 2013;DCI:10.1038/ncb2689.
description: Preparation: methanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain; distribution of epitope
Visualization methods: Hoechst 33342; Alexa Fluor 594; C-LAP
Data qualification: Processed;spatialmeasurements
description: Shown is a fluorescence microscopy image of a HeLa cell at mitotic metaphase. The cell is stained to reveal DNA (blue), microtubules (red), and the C-terminal portion of the KIF2A protein (green) which is largely confined to the compact chromosomes.
The image is part of a large project to characterize the locations of recombinantly tagged kinesin and myosin genes expressed from human or mouse-derived bacterial artificial chromosomes (BACs) as a resource for cell biology research. 
See also: Maliga et al. 2013 A genomic toolkit to investigate kinesin and myosin motor funtion in cells. Nature Cell Biol; published online Feb 2013;DCI:10.1038/ncb2689.
DOI: 10.6075/j0rj4hrc
title: CIL:437, Patiria miniata, sperm. In Cell Image Library

description: Preparation: unfixed tissue; cryofixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image; film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: intrinsic mass distribution; defocus phase contrast
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Transmission electron micrograph of unstained cryo-section of a sperm cell of the starfish Patiria miniata. Echinoderm sperm nuclei are unusual in that chromatin fibers are clearly seen, allowing their diameter to be accurately determined.
 Cryosections of frozen material are typically of low contrast and show defects such as knife marks and compression. Despite these defects, individual chromatin fibers are clearly visible, some spilling out from the nucleus. A portion of a mitochondrion is seen at upper right.
description: Whole sperm from the starfish P. miniata were cryo-fixed by plunging into liquid ethane, thin cryosections prepared, and examined in the frozen hydrated state using a Philips CM12 TEM operated at 80KV. Low dose images were recorded on SO-163 film.
See also: Woodcock CL 1994 Chromatin fibers observed in situ in frozen hydrated sections. Native fiber diameter is not correlated with nucleosome repeat length. J Cell Biol 125:11-9.
DOI: 10.5281/zenodo.17288556
title: Notas de leitura do processo "Construcción de 48 unidades escolares en Jerez de la Frontera [1971-72]" existente no Archivo Municipal de Jerez de la Frontera, em Jerez de la Frontera (Cádiz).

description: Notas de leitura do processo “Construcción de 48 unidades escolares en Jerez de la Frontera [1971-72]” existente no Archivo Municipal de Jerez de la Frontera, em Jerez de la Frontera (Cádiz). Registo efetuado em 2024.02.28 no âmbito do projeto de investigação ReARQ.IB – Built Environment Knowledge for Resilient, Sustainable Communities: Understanding Everyday Modern Architecture and Urban Design in the Iberian Peninsula (1939-1985) (ERC GA949686) e publicado online em https://arquitecturaaqui.eu/pt/documentacao/processos/31101/construccion-de-48-unidades-escolares-en-jerez-de-la-frontera-1971-1971-72. 

Dados exportados da plataforma Arquitectura Aqui (https://arquitecturaaqui.eu), repositório do referido projeto, em outubro de 2025.
DOI: 10.5281/zenodo.17288557
title: Notas de leitura do processo "Construcción de 48 unidades escolares en Jerez de la Frontera [1971-72]" existente no Archivo Municipal de Jerez de la Frontera, em Jerez de la Frontera (Cádiz).

description: Notas de leitura do processo “Construcción de 48 unidades escolares en Jerez de la Frontera [1971-72]” existente no Archivo Municipal de Jerez de la Frontera, em Jerez de la Frontera (Cádiz). Registo efetuado em 2024.02.28 no âmbito do projeto de investigação ReARQ.IB – Built Environment Knowledge for Resilient, Sustainable Communities: Understanding Everyday Modern Architecture and Urban Design in the Iberian Peninsula (1939-1985) (ERC GA949686) e publicado online em https://arquitecturaaqui.eu/pt/documentacao/processos/31101/construccion-de-48-unidades-escolares-en-jerez-de-la-frontera-1971-1971-72. 

Dados exportados da plataforma Arquitectura Aqui (https://arquitecturaaqui.eu), repositório do referido projeto, em outubro de 2025.
DOI: 10.6075/j01n818b
title: CIL:43601, Homo sapiens, lymphocyte. In Cell Image Library

description: Stained sections were recorded with a CCD camera mounted on a Nikon Eclipse 80i light microscope using a 40x objective lens.
description: Shown is a hematoxylin and eosin stained section through a plasmablastic lymphoma of the oral cavity in an HIV-positive adult male. There is a diffuse proliferation of large neoplastic cells most of which resemble B immunoblasts, plasmablasts or atypical plasma cells.
description: Preparation: formaldehyde fixed tissue; tissue in wax embedment
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: bright-field microscopy
Parameter imaged: absorption of illumination
Source of contrast: differences in adsorption or binding of stain
Visualization methods: hematoxylin; eosin
DOI: 10.6075/j0ww7ht3
title: CIL:43501, Homo sapiens, cervical epithelium. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue; tissue in plastic embedment
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain; distribution of epitope
Visualization methods: osmium tetroxide; lead salt; horseradish peroxidase; colloidal gold-conjugated antibody
Processing history: film digitized with by scanner; brightness/contrast and annotations added in Adobe Photoshop 5.0
Data qualification: Processed;spatialmeasurements
description: Epidermal growth factor receptors were labelled with an antibody conjugated to 10 nm gold, applied to the cell surface of HeLa cells, and stimulated with EGF, which causes internalization of the receptors and attached gold. The image was taken 5 minutes after internalization, at which point most of the EGFR-gold has reached early endosomes (black dots, marked by arrowheads), but has not yet entered late endosomes or lysosomes. The cells were also loaded with transferrin conjugated to horseradish peroxidase (TfHRP). The HRP catalyses a reaction in the presence of DAB that produces an electron dense product in the transferrin-containing compartments in the image. After a 1h preincubation in serum-free medium, cells were exposed to TfHRP and then incubated with EGF and anti-EGFR 10 nm gold-conjugated antibody for 30 minutes at 4C, washed, and incubated at 37C for a further 5 minutes, all in the presence of TfHRP. Cells were then room temperature fixed in 2% PFA/1.5% glutaraldehyde, a DAB reaction was carried out, and the cells were osmium stained, tannic acid treated, dehydrated, embedded en face in epon, and ~70 nm sections were cut and observed in a Philips 400 TEM. Images were recorded on film and subsequently digitized with a Flextight Precision II scanner (Imacon). Images were processed for brightness/contrast and annotations in Adobe Photoshop 5.0

 See also: Doyotte, A., Russell, M.R.G., Hopkins, C.R., Woodman, P.G. (2005) Depletion of TSG101 forms a mammalian "Class E" compartment: a multicisternal early endosome with multiple sorting defects. J. Cell Sci, 118:3003-3017
description: Transmission electron micrograph of a thin section of a HeLa cell treated to reveal components of the endocytic pathway. Epidermal growth factor (EGFR) is labeled with 10 nm immuno-gold particles and the localization of transferrin (Tf) is seen as an electron dense product as a result of treatment with Tf conjugated to horse radish peroxidase followed by diamino benzidine. E, early endosome M, late endosome (multivesicular body) L, lysozome Arrowheads denote gold particles Scale bar 500 nm
DOI: 10.6075/j0319v82
title: CIL:43451, Homo sapiens, carcinoma. In Cell Image Library

description: Digital holographic microscopy video showing cell division of unlabeled JIMT-1 breast cancer cells. During the video, spanning over 72 hours, one cell divides into three daughter cells (seen on top of the cell cluster in the upper right portion of the image). One of the daughter cell dies, and two cells merge. The
 height of the cells is color coded by the vertical look up bar on the left of the image.
description: The JIMT-1 cells were seeded on a Ibidi[TM] (Ibidi Gmbh Martinsried,Germany), one well slide and left to incubate for one day (5% CO2, 90% humidity, 37 degrees C).
The Ibidi slide was placed on a Ibidi heating plate, set to 37 degrees C, and onto the stage of the HoloMonitor M3 (Phase Holographic Imaging AB, Lund Sweden). 
One image every 4th minute was captured for a total of 72h. 
 
The Hstudio (Phase Holographic Imaging) software was used to color the images and to create an AVI movie of 8 frames/minute. No further processing was performed on the images.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: digital holographic microscopy
Parameter imaged: Phase shift of the laser light passing through the cell
Processing history: Hstudio software (Phase Holographic Imaging AB)
DOI: 10.6075/j0959hq0
title: CIL:43417, Mus musculus, mammary adenocarcinoma. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Wound Healing Assay
Time series DIC images of mouse DA3 cells, derived from the mouse mammary adenocarcinoma cell line D1-DMBA-3, induced in BALB/C mice by dimethylbenzanthracene were grown to 90% confluence. A scratch approximately 300um wide was made in the cell monolayer, and images were recorded every 14.5 min for 26 hr.
This time series image, obtained with PHA and HGF/SF treatment, is part of a group of 17 time series images (CIL:43401 to CIL:43417) representing three different treatments: (1) no HGF/SF (CIL:43406 to CIL:43411), (2) with HGF/SF (CIL:43401 to CIL:43405), activating HGF/SF-Met signaling, and (3) with PHA (Met inhibitor) and HGF/SF (CIL:43412 to CIL:43417). The group also includes two movies (CIL:43418 and CIL:43419) created from the time series CIL:43402 and CIL:43406 respectively.
description: DA3 cells expressing the fluorescent protein mCherry were grown to 90% confluence in wells of 2 cm diameter in DMEM supplemented with 10% heat-inactivated FCS (Gibco-BRL) and treated with or without the Met inhibitor PHA665752 (2.5 µM) for 2 hrs. A scratch was generated using a 200 µl tip, and the cells were incubated with or without 80 ng ml-1 Met-Hepatocyte Growth Factor/Scatter Factor (HGF/SF) and subjected to time lapse confocal laser scanning microscopy (CLSM-510, Zeiss, Germany) for approximately 26 hrs, with images taken at 14.5 min intervals. The position of each scratch was predefined, and a macro that repetitively positions the microscope on each point was executed. The acquired differential interference contrast (DIC) channel of the time-lapse sequence (shown here) was used for the multi-cellular analysis; the red fluorescence channel was exploited for single cell tracking.
See also: Zaritsky A, Natan S, Ben-Jacob E, Tsarfaty I (2012). Emergence of HGF/SF -induced Coordinated Cellular Motility. PLOS ONE 7(9): e44671