cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0rj4hmk
title: CIL:12977, Paramecium multimicronucleatum, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: The cortex of Paramecium consists of a plasma membrane and alveolar sacs, with their inner and outer alveolar membranes that limit the area in which endocytosis can easily occur to only the parasomal sacs. Parasomal sacs are cylindrical indentations of the plasma membrane that pass through the alveoli, not by penetrating through the sac but by passing through the septum. A short branch of the septum passes around the parasomal sac. In some areas the parasomal sacs extend almost perpendicularly from the basal bodies (not shown in this micrograph). There is one parasomal sac per surface depression in non-dividing cells. Rough ER, mitochondria, peroxisomes, trichocysts, and kinetodesmal fiber stack are seen in this image. The cell was incubated in hydrogen peroxide and diaminobenzidine to label the peroxisomes. TEM taken on 2/27/81 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 10,250X. Bar = 0.5µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. An unprocessed, high resolution version of this image (CIL:12610) is in the library and available for quantitative analysis. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt; diaminobenzidine
Processing history: film; Print from negative scanned for Photoshop.
Data qualification: Processed
DOI: 10.15468/dl.etdak6
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Persicaria lapathifolia salicifolia"
 ]
}

 The dataset includes 15 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009241-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j09022zc
title: CIL:16232, Prochloron. In Cell Image Library

description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: whole mounted tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Data qualification: Raw;spatialmeasurements
description: Prochloron was collected at Coconut Island, Oahu, Hawaii. Green colonies of didemnid ascidians, Diplosoma virens, were collected from shallow waters. Green spherical cells, identified as Prochloron, were released from the ascidians by gently pressing on the colonies while flushing the surface with sea water. Cells were centrifuged, then rinsed in filtered sea water fixed with glutaraldehyde, infiltrated with glycerol and vitrified. Samples were fractured and replicated using a Balzers BA 360 freeze-etch device and examined and in a JEOL 100C TEM at 50,000X magnification. Images were recorded on film and digitized.
description: Freeze-fracture replica of the unicellular photosynthetic prokaryote Prochloron showing the distribution and size of particles on cleaved thylakoid membranes. 
This image group includes many other freeze-fracture images of Prochloron.

See also: Giddings TH, Withers NW, Staehelin LA.1980 Supramolecular structure of stacked and unstacked regions of the photosynthetic membranes of Prochloron sp., a prokaryote. Proc Natl Acad Sci U S A. 77:352-3566.
DOI: 10.6075/j0nv9j8k
title: CIL:32060, Homo sapiens, osteocarcenoma. In Cell Image Library

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: 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: 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/j06q1xc1
title: CIL:39607, Saccharomyces cerevisiae. In Cell Image Library

description: 10-hour timelapse of Wild-type Saccharomyces cerevisiae growing in 2% raffinose. These experiments are the control experiments used for comparison to the effects of the double mutant Clb2dbŒî, Clb5Œî on the cell cycle control system in budding yeast. The images from two experiments done with Wild-type Saccharomyces cerevisiae are available as CIL:39606-39625 and CIL:39646-39665. The images from two experiments done with the double mutant Clb2dbŒî, Clb5Œî are available as CIL:39626-39645 and CIL:39666-39685.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: phase contrast microscopy
Parameter imaged: elastic scattering of photons
Source of contrast: differences in amount of elastic light scattering
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Images were collected at 4-minute intervals on a DeltaVision system equipped with a with a 60x PlanApo
PH3 phase-contrast, oil immersion objective (NA = 1.4). This system has a motorized x-y-z stage, automatic focusing, motorized illumination shutters and a CoolSNAP_HQ2 camera.
DOI: 10.6075/j0kk9b04
title: CIL:206, Haemanthus katharinae, endosperm. In Cell Image Library

description: Lily mitosis. A light microscope image of a cell from the endosperm of an African globe lily Haemanthus (Scadoxus) katherinae. This is one frame of a sequence that shows all phases of mitosis. The lily is considered a good organism for studying cell division because its endosperm has a liquid phase and chromosomes are thick and easier to see than human ones. Staining shows microtubules in red and chromosomes in blue.
 This image showing a cell in metaphase is the 6th of a grouped series that spans mitosis.
description: See: De Mey J, Lambert AM, Bajer AS, Moeremans M, De Brabander M. Visualization of microtubules in interphase and mitotic plant cells of Haemanthus endosperm with the immuno-gold staining method. Proc Natl Acad Sci U S A. 1982 79:1898-902.
description: Item type: recorded image
Imaging mode: bright-field microscopy
Parameter imaged: absorption of illumination
Source of contrast: differences in adsorption or binding of stain
DOI: 10.6075/j09w0fb2
title: CIL: 54681, Drosophila melanogaster, astrocytes (red). In Cell Image Library

description: Astrocyte-specific RFP expression was achieved using driven using the Gal4-UAS binary system and the driver alrm. Cortex-glia specific GFP was achieved using the lexA-lexAop binary system and the cortex-glia specific driver wrapper932i-LexA (Coutinho-Budd et al., 2017). The larval CNS was dissected in the third instar larval stage, fixed with methanol, stained for RFP, GFP and Elav (neuronal nuclei marker), and mounted in VectaShield reagent. Slides were imaged on an Innovative Imaging Innovations (3i) spinning disk confocal microscope equipped with a Yokogawa CSX-W1 using a 63X oil objective.

Staining: Astrocytes (red); Cortex glia (green); Neurons (blue)
description: Imaging mode: fluorescence microscopy
Visualization methods: Spinning Disk Confocal Imaging
description: Confocal image of the CNS of a D. melanogaster in the third instar larval stage after αSNAP KD, 18uM from the ventral surface, depicting astrocytes (red), cortex glia (green) and neuronal nuclei (blue). Our study examined the breakdown of the spatial segregation between cortex glia and astrocytes after disruption of cortex glial morphology. After knockdown of αSNAP, a protein part of the vesicual transport pathway, we observed aberrant infiltration by astrocytes into the cortex.
DOI: 10.6075/j0gx4b50
title: CIL: 53154, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given image
description: Image 4, z=16 from SC_030
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
DOI: 10.6075/j0tt4ppx
title: CIL:13544, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: whole mounted tissue
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: Helix Pomatia Lectin (HPL) (green) staining at the Golgi (Giantin) (red) in unstimulated HeLa cells. HPL binds various glycans but the Tn antigen in particular. The Tn antigen refers to terminal α-linked N-acetyl galactosamine residues (GalNAc) linked to Ser or Thr residues. Image also includes anti-GalNacT1 staining (gray). 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-Giantin, Alexa 594 for anti GalNac-T1), Hoechst (blue) and Alexa 647-conjugated-HPL was 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, 561 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 1A in J Cell Biol. 189: 843-858. 2010. Images in Fig 1 include CIL#s 13543, 13544, 13545, 13546.
DOI: 10.6075/j0kk9bm6
title: CIL: 54612. In Cell Image Library

description: Drosophila antennae were prepared as described in Tsang et al. After cryofixation by high-pressure freezing and freeze-substitution in a cocktail containing uranyl acetate and glutaraldehyde, cryofixed antennae were rehydrated gradually at ice temperature. Rehydrated samples were then subjected to DAB labeling reaction and stained using a high-contrast en bloc staining protocol. Next, the samples were dehydrated for resin infiltration and embedded in Durcupan epoxy, followed by imaging with X-ray microscopy and then serial block-face scanning electron microscopy.

The antenna was imaged using a Zeiss Merlin scanning electron microscope equipped with a Gatan 3View2XP and OnPoint backscatter detector. Images were acquired at 2.0 kV accelerating voltage with a 30 μm condenser aperture and 1.0 μsec dwell time; Z step size was 40 nm; pixel size was 4.38 nm; raster size was 14k x 16k; Z dimension was 999 sections, and local gas injection was set to 85%. Volume was aligned using cross correlation, segmented, and visualized using IMOD.
description: The biophysical properties of sensory neurons are influenced by their morphometric and morphological features, whose precise measurements require high-quality volume electron microscopy (EM). However, systematic surveys of these nanoscale characteristics for identified neurons are scarce. Taking advantage of the CryoChem method, which permits high-quality ultrastructural preservation of cryofixed and genetically labeled samples for volume EM, we acquired serial block-face scanning electron microscopy (SBEM) images of antennal tissues in which select ORNs expressed the APEX2 EM marker. These SEBEM datasets allow a systematic morphometric and morphological analysis of identified olfactory receptor neurons in Drosophila melanogaster.
description: Item type: recorded image
Imaging mode: serial block face SEM (SBFSEM)
DOI: 10.6075/j0s46rc8
title: CIL: 50938, Trypanosoma (Trypanozoon) brucei, T. brucei cells. In Cell Image Library

description: Wild type Trypanosoma brucei cells (Strain 427) were high pressure frozen and visualized through transmission electron microscopy (TEM). The images show the nucleus of the cells and the black arrow indicates nuclear envelope budding events.
description: Imaging mode: transmission electron microscopy (TEM)
Visualization methods: Stain with Uranyl acetate and Lead citrate
DOI: 10.6075/j0js9q81
title: CIL:37093, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EYFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Specifications of the custom built two-photon microscope, including the laser sources, signal amplification, PMT specifications, and YFP filter sets are described in: 
Ruthazer ES, Li J, Cline HT. 2006. Stabilization of axon branch dynamics by synaptic maturation. J Neurosci 26(13):3594-3603. 

The methods of cell transfection with electroporation can be found here: 
Bestman JE, Ewald RC, Chiu S-L, Cline HT. 2006. In vivo single-cell electroporation for transfer of DNA and macromolecules. Nat Protocols 1(3):1267-1272. 

Further explanation can be found here:
Bestman JE, Cline HT. 2008. The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo. Proc Natl Acad Sci U S A 105(51):20494-20499.

Bestman JE, Cline HT. 2009. The Relationship between Dendritic Branch Dynamics and CPEB-Labeled RNP Granules Captured in Vivo. Front Neural Circuits 3:10.
description: This is IMAGE #3 (day 3) of a time lapse series contained with in this image group. It is a neuron from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47. 
 
 The images were acquired daily over 3 days and show dendritic arbor development and morphological plasticity of the dendritic arbor with branch additions and retractions.
 
 The cell was transfected with in vivo electroporation of plasmid DNA encoding eYFP ~24 hours before the first image was acquired. The intact, living tadpole was anesthetized, positioned under a glass coverslip and this image was taken directly through its transparent skin using a custom built two-photon microscope.
DOI: 10.15468/dl.ka4x28
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Kaschgaria brachanthemoides"
 ]
}

 The dataset includes 10 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009242-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0wm1cxr
title: CIL: 52291, 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=4, y=1, z=14 from BL_024216_Myc_Terc
DOI: 10.6075/j0q81bm9
title: CIL:45916, Homo sapiens. In Cell Image Library

description: Plate 25723 - 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/j0xg9r79
title: CIL:36364, Rattus norvegicus, astrocyte, astrocyte of the hippocampus. In Cell Image Library

description: Male Sprague Dawley rats, 4 weeks of age, 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 5% aq. Lucifer Yellow. The astrocytes were filled using 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) 60x 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.
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
Data qualification: Processed;spatialmeasurements
description: Intracellular dye injections of protoplasmic astrocytes from the CA1 region of hippocampus of a 4 week old rat reveals highly ramified spongiform processes. Astrocytes were filled with Lucifer Yellow. Optical sections were generated with a single photon confocal microscope, and compiled here as a single 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.