cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j02v2f35
title: CIL:32146, Drosophila melanogaster, epithelial cell. In Cell Image Library

description: Relation to intact cell: dispersed cells in vitro
Item type: recorded image; hand drawn contour
Imaging mode: fluorescence microscopy
Parameter imaged: distribution of a specific protein; distribution of DNA
Source of contrast: distribution of a specific protein
Processing history: unprocessed raw data; tracing
Data qualification: Raw
description: Drosophila melanogaster Kc167 cells were stained for DNA (to label nuclei, red) and actin (a cytoskeletal protein, to show the cell body, green). Each image is a dual channel fluorescent image followed by a line tracing of the nuclei and a line tracing of the cell boundary. These images are provided as a tool for testing algorithims to find nuclei and the boundaries between adjacent cells.

Chris Gang outlined the nuclei and cells.
Please use the following recommended citation when using this data. "We used the Drosophila Kc167 2 image set (Jones et al., Proc. ICCV Workshop on Computer Vision for Biomedical Image Applications, 2005), available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
description: Images were acquired using a motorized Zeiss Axioplan 2 and a Axiocam MRm camera, and are provided courtesy of the laboratory of David Sabatini at the Whitehead Institute for Biomedical Research. Each image is roughly 512 x 512 pixels, with cells roughly 25 pixels in diameter, and 80 cells per image on average. 

Algorithms for finding boundaries between adjacent cells may use the union of the manually outlined cells as input. They may also use the manually outlined nuclei as seed regions. This ensures that the algorithms are compared according to their ability to find boundaries betwen adjacent cells, and not the orthogonal problems of segmenting nuclei and distinguishing foreground (cells) from background.

To compare an algorithm's results to the manual outlines, define the relevant boundary pixels as the pixels that are on the boundary found by the algorith and that are not adjacent to any background pixels. For each relevant pixel, compute the Euclidean distance to the corresponding pixel on the manually found outline. Report the percentage of relevant pixels that are within two pixels of the corresponding pixel on the manually found outline.
DOI: 10.6075/j0c53kpq
title: CIL: 54793, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Imaging mode: confocal laser scanning microscopy
Visualization methods: confocal fluorescence imaging
description: DAPI staining
description: Confocal fluorescent imaging
DOI: 10.6075/j0qj7gg6
title: CIL:10437, Rana catesbeiana, barrier epithelial cell. In Cell Image Library

description: This group of micrographs illustrate the ultrastructural characteristics of the middle layer of the three meningeal layers that cover the central nervous system The arachnoid cells contain abundant intermediate filaments that occupy a substantial volume of the cytoplasm. In some cells the intermediate filaments are organized into numerous coils of relatively uniform size and orientation. The coils appear to stack in loose hexagonal arrays. The plasma membrane of these cells has many caveolae. Adjacent arachnoid cells are connected by large desmosomes, as shown in this micrograph. Images were recorded using a Philips EM301 TEM at 80 kv. Original glass plates were scanned and digitized using an Epson V750 flatbed scanner with a step size of 15 micrometers. This group of images complement those published in the reference below. Reference: Michaels, JE, Tornheim, PA. Cell Tissue Res. 236:693-697 (1984).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Visualization methods: uranyl salt; lead salt; osmium tetroxide
Processing history: unprocessed raw data
DOI: 10.6075/j09g5mf7
title: CIL: 53390, Plankton. In Cell Image Library

description: 128x128 segmented image from volumetric hologram
description: Dinoflagellate
description: Imaging mode: Holography
Visualization methods: Amplitude Mode
DOI: 10.6075/j0fq9w1b
title: CIL: 51274, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

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
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/j0sj1k49
title: CIL: 52344, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given tile position
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: Tile x=3, y=2, z=4 from BL024199_Myc_Terc
DOI: 10.6075/j03n227n
title: CIL:41472, Phalangium opilio, optic nerve. In Cell Image Library

description: A frontal section of Phalangium opilio (Daddy Longlegs/Harvestman) eyes. The lenses (two large ovals), retinas and optic nerves are visible. The image is a depth color-coded projection of a confocal image stack. First Prize, 2010 Olympus BioScapes Digital Imaging Competition©.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Processing history: color-coded depth projection
DOI: 10.6075/j0ft8kb9
title: CIL:40360, Rattus norvegicus, oligodendrocyte. In Cell Image Library

description: This fluorescent micrograph is part of an image group displaying the morphological changes associated with a developing oligodendrocyte. The progression of images starts with CIL:40358 where cells display a relatively bipolar morphology to CIL:40359 where the actin cytoskeleton becomes very prominent to CIL:40360 where the actin coalesces and interlinks and finally there is CIL:40361 where one can observe the formation of a flattened lamellar structure which in vitro mimics the myelin sheet.
description: Preparation: formaldehyde 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: phalloidin; primary antibody plus labeled secondary antibody; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: unprocessed raw data
description: Rattus norvegicus oligodendrocytes purified from P2 cortex. Cells were fixed on glass coverslips with 4% PFA and immunostained with Phalloidin-FITC (green), alpha-tubulin primary ab./Rhodamine secondary ab (red), RIP (oligodendrocyte marker) primary ab/Cy5 secondary ab (blue), and DAPI (nuclear marker also in blue). Photographed using Leica DMI4000B microscope and 63x HCX PL APO OIL Objective. Voxel size 0.1um.
DOI: 10.5281/zenodo.17287875
title: Notas de leitura do processo "Reforma de Ambulatorio Nuestra Señora del Valle [1986-87]" existente no Archivo Municipal de Écija, em Écija (Sevilha).

description: Registo efetuado em 2024.08.23 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/48497/reforma-de-ambulatorio-nuestra-senora-del-valle. 

Dados exportados da plataforma Arquitectura Aqui (https://arquitecturaaqui.eu), repositório do referido projeto, em outubro de 2025.
DOI: 10.5281/zenodo.17287876
title: Notas de leitura do processo "Reforma de Ambulatorio Nuestra Señora del Valle [1986-87]" existente no Archivo Municipal de Écija, em Écija (Sevilha).

description: Registo efetuado em 2024.08.23 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/48497/reforma-de-ambulatorio-nuestra-senora-del-valle. 

Dados exportados da plataforma Arquitectura Aqui (https://arquitecturaaqui.eu), repositório do referido projeto, em outubro de 2025.
DOI: 10.6075/j0222ssb
title: CIL:7240, Homo sapiens, epithelial cell. In Cell Image Library

description: Preparation: methanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: primary antibody plus labeled secondary antibody; labeled primary antibody; Fluorescein (FITC); Alexa Fluor 594
Processing history: unprocessed raw data
description: HeLa cell was fixed by MeOH and stained with microtubules (green) and central spindlin protein MKLP1 (red). MKLP1 (mitotic kinesin-like protein) was well aligned on midzone microtubules during cytokinesis.
Cells were fixed with MeOH on ice for 3 min, and stained with a primary antibody against MLKP1 and FITC labeled DM1a antibody against microtubules. Secondary antibody was Alexa 594 for MLKP1. A single section was collected with a spinning disk microscope on a Nikon TE-2000 with a 1.3 NA 100X objective. Images were collected wti an OrCA ER CCD camera.
Lasers and filters: Innova 70C Spectrum 3 watt Laser, 488 Laser/ATOF 525/50, and 568 Laser/ATOF 605/52.
DOI: 10.6075/j03x856g
title: CIL:49183, 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 375 microtiter plates. Each plate has 384 wells. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale 16-bit TIFF image file.

The experiment consists of 375 microtiter plates. Each plate has 384 wells. 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 24357 - 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. 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 experiment consists of 375 plates in 384-well format, for a data set comprised of 988,994 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 approximately 5 million image files in 16-bit TIFF format.
DOI: 10.6075/j05719st
title: CIL:13886, Saccharomyces cerevisiae. In Cell Image Library

description: Constitutive targeting of Tem1 to the spindle pole body (SPB) in metaphase cells (CIL# 13883) and anaphase cells (this image). tem1Δ::GAL-UPL-TEM1 cells expressing eGFP-CNM67–TEM1 from a CEN plasmid were grown on 2% raffinose/2% galactose. Image shows localization of Cnm67-Tem1 (eGFP, green) in anaphase after cells were transferred to medium with 2% glucose. Tem1 normally localizes preferentially to the SPB that enters the daughter cell during anaphase (CIL# 13882, 13885). Cnm67 is an integral component of the outer plaque of the SPB and the Cnm67-Tem1 fusion is found to be symmetric from SPB duplication until the end of mitosis. Nuclear morphology was assessed by DAPI (blue). A differential interference contrast (DIC) image is also shown (gray). The tem1Δ::GAL1-UPL-TEM1 strain allows for the rapid, conditional depletion of Tem1. UPL, which stands for ubiquitin-proline-LacI, acts as a destabilizing module that permits rapid degradation of appended proteins. Image is Fig 1B, middle panels, in J Cell Biol. (2011) 192: 599-614. Other images in Fig 1 include CIL #13882, 13883, 13884, 13885, 13886, 13887.
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: 4',6-diamidino-2-phenylindole (DAPI); EGFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Cells (MATa tem1::GAL-UPL-TEM1-TRP1 pRS316::eGFP-CNM67–TEM1) 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.
DOI: 10.15468/dl.vjwe94
title: Occurrence Download

description: A dataset containing 580 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "Country is Spain",
 "Geometry POLYGON((-4.04649 40.33604,-4.00263 40.33604,-4.00346 40.35668,-4.047 40.35626,-4.04649 40.33604))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year 2020-2025"
 ]
}

 The dataset includes 580 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009716-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0cf9q7k
title: CIL:40079, Rattus norvegicus, astrocyte, astrocyte of the hippocampus. In Cell Image Library

description: Projection through merged optical section series of a filled astrocyte (green) in the molecular layer of the dentate gyrus of a 1 month-old rat, stained for NCAM (red), showing the relationship between astrocyte processes and laminar boundaries revealed by NCAM staining. Optical sections were generated with a single photon confocal microscope. Original data contributed to Bushong EA, Martone ME, Ellisman MH. Examination of the relationship between astrocyte morphology and laminar boundaries in the molecular layer of adult dentate gyrus. J Comp Neurol. 2003 Jul 21;462(2):241-51. PMID: 12794746. This image has been downsampled from the raw data image which can be accessed using the link provided to the Cell Centered Database.
description: 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 then ready to be immunolabeled. The rat anti-N-CAM monoclonal antibody (isoclone 12F11) was obtained from BD PharMingen (San Diego, CA), and detected using Alexa 488. Slices were coverslipped using Gelvatol (Harlow and Lane, [1988]) and allowed to set overnight at room temperature before they were examined.
Image acquisition and analysis: Specimens were examined using a Radiance2000 laser scanning confocal system (Bio-Rad, Hercules, CA) attached to a Nikon E600FN microscope (Kanagawa, Japan). A 60x oil immersion (NA 1.4) objective was used to image LY-filled astrocytes.
description: 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; Alexa Fluor 488
Data qualification: Processed
DOI: 10.6075/j0qn6699
title: CIL: 52539, 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=10 from BL32077_Myc_Terc
DOI: 10.6075/j09k49f5
title: CIL:9825, Opercularia [NCBITaxon:168247], Opercularia coarctata, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. A print of the negative was scanned and processed in Photoshop. This image is suitable for qualitative analysis. There is a high resolution version of this image in the library (CIL:39172) which is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: The peristome is covered on one side by the oral cilia and on the opposite by the ribbed wall. Lamellae from the ribbed wall extend into the nascent food vacuole forming region, the cytopharynx. This cell was not feeding and had no food vacuoles. TEM taken on 6/10/69 by R. Allen with Philips 300 operating at 60kV. Neg. 5,000X. Bar = 1µm.
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; Print from negative scanned for Photoshop
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j0x34wws
title: CIL:41726, Cricetulus griseus, ovary. In Cell Image Library

description: CHO cells at metaphase were treated with 50% D2O, fixed with glutaraldehyde, embedded in epoxy resin and 0.5 micrometer 'thick' sections stained with uranyl acetate and lead citrate for HVEM observation at 1 MeV. 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: High Voltage EM image of CHO metaphase chromosomes from a 'thick' section of metaphase-arrested cells treated with D20 to stabilize microtubules. This image was recorded with a specimen tilt of 55 degrees. The accompanying grouped image had a tilt of 45 degrees to create a stereo pair providing an oblique 3D view of the chromosomes.
description: Preparation: chemically fixed tissue
Relation to intact cell: microtome-sectioned tissue
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