cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j04f1pwg
title: CIL:9303, Rana catesbeiana, barrier epithelial cell. In Cell Image Library

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
Source of contrast: stain with broad specificity
Visualization methods: uranyl salt; lead salt; osmium tetroxide
Processing history: unprocessed raw data
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 lie parallel to the outer surface of the central nervous system, such that sections cut tangential to the membrane surface (see CIL:9301) show the spirals but transverse sections such as this one do not. The plasma membrane of these cells has many caveolae. Adjacent arachnoid cells are connected by large desmosomes.

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).
DOI: 10.6075/j0g44p4r
title: CIL:41919, triceratops, bone. In Cell Image Library

description: Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: polarized light illumination
Parameter imaged: retardance
Source of contrast: intrinsic birefringence
description: Polarized light micrograph of Triceratops dinosaur parietal (skull) bone. Honorable Mention, 2009 Olympus BioScapes Digital Imaging Competition©.
DOI: 10.6075/j0pk0g8w
title: CIL:40146, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Tissue came from either mice genetically engineered to overexpress a mutant form of human alpha synuclein (A53T) (mouse strain, C57BL/6-DBA/2; group ID, A53T15+), or wild type animals from the same strain, anesthetized with nembutal, and perfused with 4% paraformaldehyde. Tissue was sectioned on a vibratome at a thickness of 80µm and immunostained with the following antibodies: mouse monoclonal anti-alpha-SYN; BD Transduction Laboratories, secondary conjugated to Alexa 488; rabbit polyclonal anti-mGluR5, Chemicon Ab. 5675, secondary conjugated to Rhodamine Red X. DAPI was dissolved in ProLong Mounting Medium and applied at the time of mounting. Section imaged using a Olympus Fluoview 1000, with a Olympus PlanApo 60X 1.4 NA objective.
description: The neostriatum of a transgenic mouse engineered to overexpress a mutant form of human alpha synuclein (A53T), immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei. This image has been downsampled from the raw data image, which can be accessed using the link provided to the Cell Centered Database. Other images in this group include transgenic mice engineered to overexpress a mutant form of human alpha synuclein (A53T), as well as examples from wild type specimens.
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: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody; Alexa Fluor 488; X-Rhodamine; 4',6-diamidino-2-phenylindole (DAPI)
Data qualification: Processed
DOI: 10.6075/j0d50m1s
title: CIL:2867, Coleps hirtus, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: This high resolution micrograph may show important features involved in calcareous plate formation within the alveoli that underlie the plasma membrane in Coleps. Densities are seen on the inner alveolar membrane at its corners with septa. These densities are not known at this time in other ciliates and may be involved in calcareous platelet formation within the alveoli or in stabilizing the surface shape. Filamentous material fills the cytosolic space between two densities. Densities occur at the corners of the alveoli with the cytosol. A Golgi complex lies next to this quartet of densities. Smooth spongiome is also observed. Microtome sections prepared at approximately 75nm thickness. TEM taken on 5/23/69 by R. Allen with Philips 300 operating at 60kV. Neg. 18,500X. The raw film was scanned with a Nikon Coolscan 9000ED. This high resolution image is suitable for quantitative analysis.

Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment
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; unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0db80fg
title: CIL:50454, Mus musculus, Mouse brain tissue, Mouse brain tissue expressing tdTomato in corticotropin releasing factor-expressing neurons. In Cell Image Library

description: Item type: recorded image
Imaging mode: confocal microscopy
description: In this study, we developed an electron microscopy method, called CryoChem, to optimally preserve the morphology of genetically labeled tissues. This method also allows us to perform 3D correlated light and electron microscopy (CLEM) in the well-preserved tissue. This dataset contains the DRAQ5 confocal volume of the CLEM experiment in a mouse brain expressing tdTomato in corticotropin releasing factor-expressing neurons.
description: Brief description of sample preparation
After cryofixation by high-pressure freezing and freeze-substitution, cryofixedmouse brain slices were rehydrated gradually. Rehydrated samples were then imaged with confocal microscopy to capture the DRAQ5 and tdTomato signals. Next, the samples were stained using a high-contrast en bloc staining protocol. Then the samples were dehydrated for resin infiltration and embedding, followed by imaging with X-ray microscopy and then SBEM.

Confocal Microscopy
After freeze-substitution and rehydration, the mouse brain slice was placed in ice-cold 0.15 M sodium cacodylate for imaging. Confocal volumes of DRAQ5 and tdTomato signals were collected on an Olympus FluoView 1000 confocal microscope with a 20X air and 60X water objectives using 561 nm and 633 nm excitation.
DOI: 10.6075/j0hq3xjt
title: CIL:27870. In Cell Image Library

description: One of the principal challenges in counting or segmenting nuclei is dealing with clustered nuclei. To help assess algorithms' performance in this regard, this synthetic image set consists of five subsets with increasing degree of clustering. Five subsets of 20 images each are provided. Each image contains 300 objects, but the objects overlap and cluster with overlap probability ranging from 0.0 to 0.6, and can be found with CIL 27833, 27853, 28754, 28734, and 28714, respectively. This image set has 0.15 probability overlap. The images were generated with the SIMCEP (http://www.cs.tut.fi/sgn/csb/simcep/tool.html) simulating platform for fluorescent cell population images (Lehmussola et al., IEEE T. Med. Imaging, 2007 and Lehmussola et al., P. IEEE, 2008). Ground truth for foreground/background segmentation are available as binary images as the second image in the tiff image stack. 
Recommended citation "We used the Synthetic 1 image set (Ruusuvuori et al., in Proc. of the 16th European Signal Processing Conference (EUSIPCO-2008), 2008), available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
DOI: 10.6075/j08052n5
title: CIL:35906, Saccharomyces cerevisiae. In Cell Image Library

description: Time-lapse images were collected on a DeltaVision system (Olympus IX71) with 60x/1.42 NA objective at 5 minute intervals. Please see the microscopy section in the referenced manuscript for details for image analysis.
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP-tagged TEM1. 
 
 TEM1 is a GTP-binding protein of the ras superfamily involved in termination of M-phase; controls actomyosin and septin dynamics during cytokinesis. 
 
These phase,gfp images are part of an image group that ranges from CIL:35900-35919. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the 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 electrons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
DOI: 10.6075/j0rr1xds
title: CIL:12850, Rattus rattus, glandular epithelial cell, milk secreting cell, mammary alveolar cell. In Cell Image Library

description: Tissue was processed for immunoelectron microscopy using a modified Tokuyasu method. Briefly, minced tissue was fixed in 4% paraformaldehyde containing 5% sucrose and 100 mM HEPES and infiltrated with PBS containing 2.1 M sucrose over 10 h, with repeated solution changes. Fixed tissue was transferred to an aluminum cryosectioning stub (Ted Pella, Inc., Redding, CA) and immediately frozen in liquid nitrogen. Semithin (90 nm) cryosections were cut at -110C with an UltraCut UCT/FCS cryomicrotome (Leica), using a diamond knife (Diatome) and transferred to a Formvar-coated, carbon-coated, glow-discharged 100-mesh copper-rhodium electron microscopy grid. Following blocking of nonspecific antibody binding sites with 10% calf serum in PBS, the sections were labeled by incubation with an antibody to MG-160 (mouse monoclonal) followed by colloidal gold-conjugated secondary antibody (10 nm anti-mouse; Ted Pella Inc., Redding, CA) and then negatively stained and embedded with 1% uranyl acetate, 1% methylcellulose in distilled water. Samples were viewed in a Philips CM10 electron microscope, and images were collected digitally. See Ladinsky and Howell (2007) for more information on methods used.
description: Immunoelectron microscopy of mammary gland tissue from lactating rats with medial cisternae of the Golgi apparatus indicated by immunogold labeling of MG-160, a 160 kDa membrane sialoglycoprotein specific to medial Golgi.
description: Preparation: cryostat-sectioned tissue; formaldehyde fixed tissue; embedded tissue; methylcellulose embedded
Relation to intact cell: 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; distribution of a specific protein
Visualization methods: gold; uranyl salt; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j01r6pq9
title: CIL:435, Patiria miniata, sperm. In Cell Image Library

description: Transmission electron micrograph of unstained cryo-section of a sperm cell of the starfish Patiria miniata. Echinoderm sperm nuclei are unusual in that chromatin fibers are clearly seen, allowing their diameter to be accurately determined.
 Cryosections of frozen material are typically of low contrast and show defects such as knife marks and compression. In this image, the nucleus at lower left has partly torn away from the rest of the cell. Despite these defects, individual chromatin fibers are clearly visible.
description: Whole sperm from the starfish P. miniata were cryo-fixed by plunging into liquid ethane, thin cryosections prepared, and examined in the frozen hydrated state using a Philips CM12 TEM operated at 80KV. Low dose images were recorded on SO-163 film.
See also: Woodcock CL 1994 Chromatin fibers observed in situ in frozen hydrated sections. Native fiber diameter is not correlated with nucleosome repeat length. J Cell Biol 125:11-9.
description: Preparation: unfixed tissue; cryofixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image; film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: intrinsic mass distribution; defocus phase contrast
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
DOI: 10.6075/j0js9q2b
title: CIL: 53416, Melosira octagona, Plankton. In Cell Image Library

description: 128x128 segmented image from volumetric hologram
description: Zooplankton
description: Imaging mode: Holography
Visualization methods: Amplitude Mode
DOI: 10.6075/j01r6p71
title: CIL:13754, Drosophila melanogaster, germ line cell, follicle cell, germ line stem cell, follicle stem cell. In Cell Image Library

description: Fly ovaries were dissected and fixed as described previously (O'Reilly et al., 2008). Primary antibodies were anti-betagalactosidase and 1:25 mouse anti-Fas3 (Developmental Studies Hybridoma Bank [DSHB]. Secondary antibodies used were either FITC, Cy3, and/or Cy5 conjugated to species-specific secondary antibodies (Jackson ImmunoResearch Laboratories, Inc.). Samples were mounted in Vectashield mounting medium. Images were collected at room temperature (22C) using 40× (1.25 NA) or 63× (1.4 NA) oil immersion lenses (Leica) on an upright microscope (DM 5000; Leica) coupled to a confocal laser scanner (TCS SP5; Leica). LAS AF SP5 software (Leica) was used for data acquisition. Images representing individual channels of single confocal slices from the center of each germarium were exported as TIFF files, and images were converted to figures using Photoshop software (Adobe).
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 emission
Source of contrast: distribution of a specific protein
Visualization methods: primary antibody plus labeled secondary antibody; beta-galactosidase
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Hedgehog (Hh, red) is transcribed in apical cells of the Drosophila wild-type germarium (CIL# 13755, 13744). In the absence of boi (boi[e] mutant), Hh protein is redistributed from apical cells to the extracellular space of the local follicle stem cell niche (CIL# 13745), but Hh transcription is still in apical cells (this image; boi[e]; Hh-lacZ). Hh transcription is demonstrated by the Hh-lacZ reporter and follicle cells are highlighted using anti-Fas-3 (green). Image is Supplemental Figure S3B in J Cell Biol. 2010. 191: 943-952.
DOI: 10.6075/j08p60kq
title: CIL:39628, Saccharomyces cerevisiae. In Cell Image Library

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: 10-hour timelapse of the double mutant Clb2dbŒî, Clb5Œî, which has the destruction box region of the CLB2 gene, on the cell cycle control system in budding yeast. The yeast, Saccharomyces cerevisia, are growing in 2% raffinose, since this mutation is inviable in glucose. The images from two experiments done with Wild-type Saccharomyces cerevisiae as a control 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: 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/j0kp818n
title: CIL:12110, Colpoda cucullus, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: This micrograph shows the striated kinetodesmal fiber extending to the pellicle from the basal body where it terminates against the epiplasm. A bundle of microtubules extends into the cell's cytosol from the basal body. Alveoli, parasomal sacs, mucocysts, and mitochondria are evident. TEM taken on 5/31/69 by R. Allen with Philips 300 operating at 60kV. Neg. 14,800X. Bar = 0.5µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. A raw, unprocessed, high resolution version of this image (CIL:2857) 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 were prepared at approximately 75nm thickness. Additional information is 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
Processing history: recorded image; film; Print from negative scanned to Photoshop.
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j0p84bm4
title: CIL: 54273. In Cell Image Library

description: TKL 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
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.
DOI: 10.6075/j0610zjd
title: CIL:1627, Caenorhabditis elegans. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 0 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/j0g16046
title: CIL:913, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Rabbit psoas skeletal muscle fibers were held at constant length and rigor induced by immersion in glycerol. The fibers were quick-frozen by contact with a liquid helium- cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 24 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

Images were recorded on Kodak 4489 film at 100,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:902.
description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
DOI: 10.6075/j0r49pkz
title: CIL:11164, Periplaneta americana, oocyte. In Cell Image Library

description: Uptake of yolk protein into coated vesicles (arrows) at the periphery of oocytes of the cockroach Periplaneta americana. Yolk protein binds to regions of the membrane with a prominent glycocalyx. Because yolk protein has a strong affinity for osmium, it is electron dense and appears prominently in electron micrographs. Images by Everett Anderson, Figures 57 (upper) and 58 (lower) from Chapter 2 (Specializations of the Free Surface) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
description: Preparation: crosslinking-fixative 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
Source of contrast: stain with broad specificity
Visualization methods: osmium tetroxide
Data qualification: Processed