cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0bk1b2t
title: CIL:13868, Saccharomyces cerevisiae. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; ethanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: widefield illumination; fluorescence microscopy; differential interference contrast microscopy
Parameter imaged: fluorescence emission; optical path length gradient
Source of contrast: distribution of a specific protein; compartmentalization of stain or label; boundaries between regions with different refractive index
Visualization methods: EGFP; 4',6-diamidino-2-phenylindole (DAPI); mCherryFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Cells (MATa tem1::TEM1-yEGFP::SpHIS5 bfa1::BFA1-mCherry-kanMX6) were fixed in 2.5% formaldehyde for 10 min, washed twice, and resuspended in 0.1 M potassium phosphate buffer, pH 6.4. Cells were then fixed for 10 min in 80% ethanol and resuspended in 1 mg/ml DAPI. 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: During late anaphase, Tem1 (green) localized to both spindle pole bodies (SPBs), but Bfa1 (red) was asymmetrically localized to the daughter SPB. DAPI (blue) and DIC (hidden) are also shown. Compare to metaphase image CIL# 13869. Image is Fig 6A, bottom panels, in J Cell Biol. (2011) 192: 599-614. Images in Fig 6 include CIL# 13869, 13868, 13871, 13870.
DOI: 10.6075/j0cr5rz0
title: CIL:48756, Mus musculus, MC38-Cerulean cancer cells. In Cell Image Library

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, MC38-Cerulean cancer cells were injected on the distal flank. This folder contains images from the tumor grown in the COL-EGFP 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.
 
Image name: 110613 COLEGFP tumor side 63x means 25x water.lif - 2
 
Project: 20389
description: Item type: confocal microscopy
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/j0gm86qx
title: CIL: 51296, 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: 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.
DOI: 10.6075/j0cf9p75
title: CIL:24567, Balamuthia mandrillaris, cell by organism, eukaryotic cell, Eukaryotic Protist, Amoeboid Protist. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: living tissue; whole mounted tissue
Item type: microscopy; in-focus phase contrast
Imaging mode: retardance; phase contrast microscopy
Parameter imaged: boundaries between regions with different refractive index
Source of contrast: boundaries between regions with different refractive index
Visualization methods: natural boundaries
Processing history: living tissue; recorded image; charge coupled device (CCD)
Data qualification: Raw
description: A frame from the grouped movie of a Balamuthia mandrillaris ameba within a culture of monkey kidney cells. Accompanying photographs are enlargements of the tips of pseudopodia to demonstrate their flexibility and movement, and a second set of photographs demonstrate the puncture of the plasma membrane of a monkey kidney cell. The first shows an indentation in the cell membrane, the withdrawal of the pseudopodia tip and the subsequent rupture of the membrane in the area indented by the amebic tip. The eventual break in the membrane may have resulted from the release of a proteolytic enzyme. Details of the preparation can be found in CIL:19325.
DOI: 10.6075/j0nk3d09
title: CIL:36590, Xenopus laevis, fertilized egg. In Cell Image Library

description: This image is part of a large data set of Xenopus laevis eggs imaged at various times post fertilization (the first number of the file name corresponds minutes, eg 30_2 is 30 min post fertilization). The embryos are stained for alpha-tubulin (green) using a directly labeled B-5-1-2 antibody and DNA (red).
description: Preparation: methanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; distribution of a specific protein
Visualization methods: labeled primary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Images collected on a Zeiss LSM 710 confocal with a 10X 0.3 NA objective using 561 and 633 laser lines.
DOI: 10.6075/j0h41q4b
title: CIL:13547, Homo sapiens, epithelial cell, cervical carcinoma. 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: single-spot confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein; distribution of epitope; compartmentalization of stain or label
Visualization methods: Alexa Fluor 647; Alexa Fluor 594; Alexa Fluor 488; primary antibody plus labeled secondary antibody; Helix pomatia agglutinin; Hoechst
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: GalNac-T1 staining (red) and Helix Pomatia Lectin (HPL) (green) colocalizes exclusively at the Golgi (Giantin) (gray) in unstimulated HeLa cells. The Tn antigen refers to terminal α-linked N-acetyl galactosamine residues (GalNAc) linked to Ser or Thr residues. HPL binds various glycans but the Tn antigen in particular. HeLa cells were serum starved overnight in DME (noFBS). Cells were fixed for 10 min (4% paraformaldehyde) and permeabilized (0.2% Triton X-100). Primary antibody staining followed the manufacturer's instructions. Cells were subsequently stained for 15–30 min with secondary Alexa Fluor–conjugated antibodies (Alexa 488 for anti-GalNac-T1, Alexa 594 for anti-Giantin). Hoechst (blue) and Alexa 647-conjugated-HPL were added during secondary antibody incubations. Cells were mounted onto glass slides using FluorSave (Merck) and imaged at room temperature using an inverted FluoView confocal microscope (model IX81; Olympus) with fluorescence excitation at 488 nm, 543 nm, and 633 nm and either a 60x objective (U Plan Super Apochromatic [UPLSAPO]; NA 1.35) or 100x objective (UPLSAPO; NA 1.40) using Immersol oil. Microscope coupled with a CCD camera (model FVII). Images were acquired and processed using Olympus FV10-ASW software. Image corresponds to Fig 2A in J Cell Biol. 189: 843-858. 2010. Images in Fig 2 include CIL#s 13547, 13548, 13549, 13550.
DOI: 10.6075/j0cc106q
title: CIL: 52532, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

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
description: One z layer of a z-stack at the given tile position
description: Tile x=7, y=1, z=3 from BL32077_Myc_Terc
DOI: 10.6075/j0h41qsv
title: CIL:41612, Cricetulus griseus, epithelial cell, ovary. In Cell Image Library

description: High Voltage Transmission EM of whole mitotic metaphase chromosomes from Chinese hamster ovary cells. This image was recorded at a specimen tilt of 49 degrees and is grouped with one taken at 59 degrees, creating a stereo pair giving an oblique 3D view of the chromosomes.
description: CHO cells arrested at metaphase with colcemid were treated with 67% D2O, in 0.07M phosphate buffer and squashed in 50% acetic acid. Preparations were transferred to EM grids and examined with the Wisconsin HVEM operated at 1MeV.
See also: H. Ris 1981 Stereoscopic electron microscopy of chromosomes. Meth Cell Biol 22:77-96 H. Ris 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:220-246.
description: Preparation: chemically fixed tissue
Relation to intact cell: squash preparation
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.5281/zenodo.13926315
title: The role of technology anxiety in the use of e-health solutions in Polish society

description: The dataset used in the analysis reported in the paper titled: "The role of technology anxiety in the use of e-health solutions in Polish society," submitted and accepted for the 23rd International Conference on Informatics Management and Technology in Healthcare, Athens, Greece, July 4-6, 2025. The paper is planned to be published in the post-conference book by IOS Press. 

This research was funded by the National Science Centre, Poland, within the project titled: "Determinants of acceptance and readiness to use of e-health applications and Health 4.0 technologies in Polish society" (grant number: 2021/43/B/NZ7/02140).
DOI: 10.5281/zenodo.13926316
title: The role of technology anxiety in the use of e-health solutions in Polish society

description: The dataset used in the analysis reported in the paper titled: "The role of technology anxiety in the use of e-health solutions in Polish society," submitted and accepted for the 23rd International Conference on Informatics Management and Technology in Healthcare, Athens, Greece, July 4-6, 2025. The paper is planned to be published in the post-conference book by IOS Press. 

This research was funded by the National Science Centre, Poland, within the project titled: "Determinants of acceptance and readiness to use of e-health applications and Health 4.0 technologies in Polish society" (grant number: 2021/43/B/NZ7/02140).
DOI: 10.6075/j0t15290
title: CIL:39135, Arabidopsis thaliana, leaf. In Cell Image Library

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: uranyl salt
Processing history: montage
Data qualification: Processed
description: See K Philippar. T Geiss, I Ilkavets, U Oster, S Schwenkert, J Meurer, J Soll 2007 Chloroplast biogenesis: The use of mutants to study the etioplast-chloroplast transition. Proc Natl Acad Sci USA 104:678-683.
description: Transmission EM of cotyledon of the double knockout oep16.1/16.4 of Arabidopsis thaliana grown in the dark and grown under a normal day/night light regime. Characteristic wildtype thylakoids are seen. Other images in this group show wildtype and knockout plastids under different light regimes.
DOI: 10.6075/j03b5zp8
title: CIL: 52658, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

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
description: One z layer of a z-stack at the given tile position
description: Tile x=6, y=2, z=3 from PS09_287383C_Myc_Terc
DOI: 10.6075/j0sx6bzv
title: CIL:11956, Halistaura cellularia, oocyte. In Cell Image Library

description: Time lapse movie showing mitosis and cleavage in fertilized eggs of the jellyfish Halistaura cellularia. The use of polarizing microscopy reveals the mitotic spindles, which are seen in bright or dark contrast depending on their orientation with respect to the polarized illumination. Nuclei are not evident during interphase.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: polarization microscopy
Parameter imaged: retardance
Source of contrast: form birefringence
Visualization methods: visualization of contiguous regions
Data qualification: Processed
description: See: S. Inoue (1964) Organization and function of the mitotic spindle. In, Primitive Motile Systems in Cell Biology. Academic Press pp 549-598.
DOI: 10.6075/j00c4vwr
title: CIL:40025, Rattus, astrocyte, astrocyte of the hippocampus. In Cell Image Library

description: Intracellular dye injections of protoplasmic astrocytes from the CA1 region of hippocampus of 3 week old rat reveals highly ramified spongiform processes that span territories with minimal overlap. Astrocytes were filled with Alexa 488 (green) and Alexa 568 (red). Optical sections were generated with a single photon confocal microscope and are presented here as a maximum projection image. 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
Visualization methods: Alexa Fluor 488; Alexa Fluor 568
Data qualification: Processed;spatialmeasurements
description: Male Sprague Dawley rats were anesthetized and perfused transcardially with with Ringer's solution (37°C), followed by 4% paraformaldehyde (PFA) in PBS (37°C, pH 7.4). Tissue was sectioned (100 µm thick) using a vibratome, and injected with a BX50WI microscope (Olympus, Melville, NY) and, using infrared differential interference contrast videomicroscopy,cells with a small diameter soma (approx. 7–11µm) in the stratum
radiatum of CA1 were located and impaled with glass micropipettes filled with either AlexaFluor 488, 20mM AlexaFluor 568 in 200mM KCl. The astrocytes were filled using a 0.5 Hz pulses of current until all of the processes were brightly fluorescent. After several astrocytes were filled, a slice was placed in the 4% PFA overnight at 4°C. Slices were then imaged after coverslipping in Gelvatol. Confocal images were acquired with a BioRad Radiance2000(Hercules, CA) attached to a Nikon E600FN (Kanagawa, Japan) microscope equipped with a Nikon (Tokyo, Japan) 60× oil objective (NA 1.4). Additional details are provided in Bushong EA, Martone ME, Ellisman MH. Maturation of astrocyte morphology and the establishment of astrocyte domains during postnatal hippocampal development. Int J Dev Neurosci. 2004 Apr;22(2):73-86.
DOI: 10.6075/j04q7v0x
title: CIL:32108, Homo sapiens, osteocarcenoma. In Cell Image Library

description: The images constitute one row of a 348 well plate. The dose curve consists of 11 dose points and one control. Each concentration is duplicated in adjacent wells. Each well has three fields.
description: This image set is of Transfluor assay where an orphan GPCR (G-protein coupled receptor) is stably integrated into a beta-arrestin GFP (green) expressing U2OS cell line also showing nucleus (red). After one hour incubation with a compound, the cells were quenched with fixative (formaldehyde) and the plate was read on Cellomics ArrayScan HCS Reader using the GPCR Bioapplication. Negative results are a more uniform distribution of GFP throughout the cytoplasm and positive results are a peri-nuclear localization.
Recommended attribution: "We used the SBS Roche Transfluor image set provided by Ilya Ravkin and available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
Analysis of the data set can be downloaded from http://www.broadinstitute.org/bbbc/sbs_roche_transfluor.html
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: plate reader
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; distribution of DNA
Visualization methods: EGFP
Processing history: unprocessed raw data
DOI: 10.6075/j0ht2p3r
title: CIL: 54549, Lilium longiflorum, reproductive cell (microsporocyte). In Cell Image Library

description: Feulgen stained light microscopy image collected using a bright field zeiss microscope, using a 100X, N.A. 1.4 Neuflar lens.
description: 4 Prophase I of meiosis, substage pachytene in a diploid lily pollen mother cell. The nucleoli are once again round, two are visible. All of the homologous chromosome regions are fully paired, appearing as double width threads.
description: Imaging mode: light micrograph
Visualization methods: DNA specific contrast staining using Feulgen staining
DOI: 10.15468/dl.a3k5ha
title: Occurrence Download

description: A dataset containing 102 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Veronica anagallis-aquatica"
 ]
}

 The dataset includes 102 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009667-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0ft8kq7
title: CIL: 54058, Homo sapiens, HeLa. In Cell Image Library

description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
description: TK family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
description: Visualization methods: confocal microscopy
DOI: 10.6075/j0k073n4
title: CIL:45840, Homo sapiens. In Cell Image Library

description: Plate 25416 - 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.