cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j06h4g2p
title: CIL:36700, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Quick-freeze deep-etch rotary-shadowed replica of a portion of the chemically-unfixed cytopharynx. The cytopharynx is continuous with the plasma membrane and is covered by only one membrane which is pleated over the ends of the cytopharyngeal microtubular ribbons. Numerous discoidal vesicles are bound single file along the anterior side only of each ribbon. This is the site where discoidal vesicles fuse with the cytopharyngeal membrane to form the digestive vacuole. TEM taken on 5/18/88 by C. Schroeder with Zeiss 10A operating at 80kV. Neg. 6,300X. Bar = 1µm. This image is suitable for qualitative analysis. There is a high resolution version of this image in the library (CIL:40510) which is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).Part published in J. Cell Biol. 111:2553-2562, 1990. Adapted with permission.
description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film; Print of negative scanned for Photoshop
Data qualification: Processed
DOI: 10.5281/zenodo.17484692
title: large ensembles of CMIP6
DOI: 10.6075/j0qj7gj3
title: CIL:1005, Caenorhabditis elegans, muscle cell. In Cell Image Library

description: C. elegans muscle age is a data set of fluorescence 20X microscopy images of C. elegans nematodes stained with phalloidin to visualize actin in muscles at different ages (1,2,4, and 8). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1005, 1057, 1105, and 1265, respectively.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: phalloidin
Processing history: unprocessed raw data
description: The purpose of the dataset C. elegans muscle aging is to deduce the age of the nemathode based on images of muscles. Images of C. elegans were taken at different chronological ages. This image is part of the day 1 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
DOI: 10.6075/j00000xj
title: CIL:41733, Arabidopsis thaliana. In Cell Image Library

description: B0008269. 2011 Collection: Wellcome Images Copyrighted work available under Creative Commons by-nc-nd 2.0 UK: England & Wales, see http://images.wellcome.ac.uk/indexplus/page/Prices.html
description: Confocal micrograph showing the tissue structures within the leaf of an Arabidopsis thaliana seedling. The sample was fixed and stained with propidium iodide, which labels DNA, and imaged four years later. Over time, oxidation of the stain differentiates the fluorescent properties in different parts of the tissue so that they can be excited with distinct wavelengths of light from a confocal microscope. The researchers are using these techniques to investigate cellular architecture in plants and gene activity. The horizontal field width of this image is 200 microns. Wellcome Image Award 2012.
description: Preparation: chemically fixed tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain; oxidation
Visualization methods: propidium iodide
DOI: 10.6075/j0mk6bgk
title: CIL:46316, Homo sapiens. In Cell Image Library

description: Plate 26569 - 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/j0sn07zk
title: CIL:8459, Rattus, multipolar neuron. In Cell Image Library

description: Development of axon and dendritic arbors in cultured hippocampal neurons after 2 days in vitro. At this timepoint, many, but not all cells are polarized, evidenced by the absence of a long, slender axon. MAP2 staining (red) is becoming segregated to the dendrites, while microtubule staining (green) reveals both the axons and dendrites in the field of view. Nonneuronal cells (e.g. glia) are infrequent, but may also be present in this preparation. 

Detailed methods: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained for tubulin (monoclonal DM1A, from Sigma with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and MAP2 (polyclonal Ab266, from S. Halpain with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 40X (HCX PL APO, NA 1.25) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. This merged image was generated with the MetaMorph color combine function.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0p55m89
title: CIL:11987, Drosophila melanogaster, epithelial cell. In Cell Image Library

description: TIRF time lapse of myosin-GFP (left), mCherry-tubulin (middle), and overlay (myosin-GFP in green and mCherry-tubulin in red) in wild-type S2 cells from metaphase to anaphase. This cell has many astral microtubules touching the cortex (within the TIRF illumination field) in the bottom left and very few in the top right. Despite this asymmetry (perhaps due to a tilting of the spindle), myosin localization occurs in a normal, symmetrical manner, and myosin clears from both poles.
Video corresponds to video 4 from J Cell Bio 186:727-738, 2009. Total internal reflection microscopy was performed using a microscope (Perfect-focus TE2000; Nikon) with a 100×, 1.45 NA objective (Nikon) and illumination from either a 488-nm argon laser (100 mW) or a 491 nm solid-state laser (100 mW) and a 561-nm solid-state laser (50 mW). For dual-color TIRF microscopy, we used a triplepass dichroic filter (z491/561/633rpc) and changed the emission filter (ET525/50 or ET595/50; both from Chroma Technology Corp.) with a filter wheel placed before the camera. In some cases, an excitation notch filter was used in the filter cube (NF01-405/488/561/635; Semrock, Inc.). Images were typically captured every 2-3 s with a 50-200 ms exposure with an EM charge-coupled device camera (iXon; Andor Technology). The microscope was controlled and images were acquired using open source MicroManager software (http://www.micro-manager.org).
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: TIRF
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP; mCherryFP
Processing history: unprocessed raw data; color combine
Data qualification: Raw
DOI: 10.6075/j05h7f97
title: CIL:9065, Nephrotoma suturalis, spermatocyte. In Cell Image Library

description: The events of meiosis I in a living insect spermatocyte beginning at metaphase with bivalents at the spindle equator, followed by anaphase onset, chromosome segregation and the start of cytokinesis. Testes from the Crane fly Nephrotoma suturalis were observed with time-lapse polarization using a Nikon Microphot SA, equipped for liquid crystal polarized light microscopy (LC-PolScope, CRi, Woburn Massachusetts) 60x/1.4 PlanApo oil immersion objective, 1.4 NA oil imm. condenser, with 1.5x zoom lens. Image acquisition and processing Camera: Images captured every 60 sec over 105 min by a QImaging Retigo EXi CCD camera. A movie prepared from this image stack is included in the grouped set.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image; charge coupled device (CCD); Processed image based on 5 recorded images
Imaging mode: polarization microscopy
Parameter imaged: UV/visible/IR photons
Source of contrast: intrinsic birefringence
Visualization methods: relative retardation (retardance) measurement
Processing history: 5-frame algorithm
DOI: 10.6075/j0q240gf
title: CIL:54918, Homo sapiens, neuron of cerebral cortex. In Cell Image Library

description: The data was collected from human brain samples from Alzheimer's disease-affected patients selected from the Neuroscience Group of Antioquia (GNA) database, University of Antioquia, Medellín, Antioquia, Colombia. Imaging was performed by first collecting a 2D map of the area of interest of the thick section and then specific areas were further investigated using multi-tilt electron tomography.
description: Item type: EM tomogram
Imaging mode: Electronic tomography
description: Brain ID 363;
Gender Female;
AAO 50;
AAD 55;
Post Mortem Time 1.8 h;
PSEN1 E280A Heterozygous carrier;
APOE R154S Christchurch Heterozygous carrier;
Area of the brain imaged: C11b, Cingulate cortex, Neuronal cell bodies
DOI: 10.6075/j0542m68
title: CIL:45992, 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 26081 - 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: 10.6075/j01z43wt
title: CIL: 51927, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: Imaging mode: DICM
Visualization methods: Spinning disc confocal DICM & widefield DICM Using a Nikon TiE microscope equipped with a 40x, 0.95 N.A. objective and a Hamamatsu ORCA-Flash 4.0 V3 Digital CMOS camera, or a Nikon TiE spinning-disc confocal microscope equipped with a Yokogawa CSU-X1 scanning unit, an Andor iXon 888 EMCCD camera, and a 60x, 1.3 N.A. water-immersion objective or a 40x, 0.95 N.A. objective
description: A novel cell population analysis to quantify both initial and long-term drug effects, namely pseudopod adaptation and recovery following an initial drug-induced perturbation, adding drug slowly in 1/4 increments over 90 minutes.
description: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
DOI: 10.6075/j01r6qmc
title: CIL:35762, Saccharomyces cerevisiae. In Cell Image 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
Processing history: unprocessed raw data
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Clb2. Clb 2 is a cyclin-dependent protein kinase regulator, involving in G2/M transition of mitotic cell cycle and positively regulating spindle pole body separation. These phase and GFP images are part of an image group containing CIL 35760-35779. Note that there are additional groups of images of other cell cycle regulator proteins by the same authors available in the Library.
description: Time-lapse images were collected on a DeltaVision system (Olympus IX71) with 60x/1.42 NA objective at 5 minute intervals. Please read the microscopy section of the referenced paper for details before image analysis.
DOI: 10.6075/j0348jzz
title: CIL: 53073, 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 image
description: Image 4, z=19 from SC_028
DOI: 10.6075/j0vq31qd
title: CIL:7743, Potorous tridactylus tridactylus, primary cell line cell. In Cell Image Library

description: Preparation: cryofixed tissue; tissue in plastic embedment; freeze substitution
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); film
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: electron-dense stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
description: Details of the Golgi apparatus seen in 40 nm epon sections of Ptk tissue culture cells after plunge freezing,and freeze substitution. Image recorded at 28,500x with a Philips CM10 TEM operated at 80KV
DOI: 10.6075/j0sb45rg
title: CIL:36300, Rattus, astrocyte. In Cell Image Library

description: Male Sprague Dawley rats, 3 weeks of age, were anaesthetized 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 5% aq. LY, 20mM AlexaFluor 568 in 200mM KCl, or 20mM AlexaFluor 488 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). Optical z resolution, 0.15 µm. 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.
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 Lucifer Yellow (green) and Alexa 568 (red) Optical sections were generated with a single photon confocal microscope.
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: lucifer yellow; Alexa Fluor 568
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j0028r1q
title: CIL: 51944, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

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

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
description: A novel cell population analysis to quantify both initial and long-term drug effects, namely pseudopod adaptation and recovery following an initial drug-induced perturbation, adding drug slowly in 1/4 increments over 90 minutes.