cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0513x6b
title: CIL:36266, Vorticella convallaria, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Accumulation of golgi cupulas near a food vacuole. The food vacuole shown has already fused with many vesicles that have already added their membrane as well as their dense inner lining to the vacuole lumen. TEM taken on 2/17/72 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 19,500X. Bar = 0.5µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. There is a high resolution version of this image in the library (CIL:39458) which is available 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; 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
description: 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/).
DOI: 10.5281/zenodo.17302967
title: Kachhi Plain Basin Runoff

description: Kachhi Plain Basin Runoff 

Dataset Description

The processed datasets for the three rivers are organized in three separate Excel files, where sheet D1 corresponds to the Nari River, sheet D2 to the Bolan River, and sheet D3 to the Mula River, ensuring a structured and accessible format for modeling and analysis.

The dataset developed for this study covers the Kachhi Plain Basin, which includes the Nari, Bolan, and Mula Rivers, where no gauging stations are available to provide observed discharge records. Daily precipitation data were obtained from the ERA5 reanalysis product at a spatial resolution of 25 km for the period 2011–2022.

Catchment characteristics were derived from multiple sources: land use and land cover information were extracted from the ESRI Land Use/Land Cover dataset, soil properties were obtained from the FAO soil database, and watershed topography was defined using the USGS digital elevation model (DEM).

These datasets were integrated within the HEC-HMS hydrological model to simulate daily runoff at the basin outlet. The simulated runoff was initially produced in units of mm³/day and was subsequently converted into m³/s to align with standard hydrological practice. Since the basin lacks direct discharge observations, this HEC-HMS simulated runoff served as the proxy observed dataset for further analysis.

Note: This dataset is freely accessible for educational and research purposes only. Users who employ are requested to reference/cite this dataset with proper acknowledgement and cite the corresponding DOI (10.5281/zenodo.17302968) in their publications/reports etc.
DOI: 10.5281/zenodo.17302968
title: Kachhi Plain Basin Runoff

description: Kachhi Plain Basin Runoff 

Dataset Description

The processed datasets for the three rivers are organized in three separate Excel files, where sheet D1 corresponds to the Nari River, sheet D2 to the Bolan River, and sheet D3 to the Mula River, ensuring a structured and accessible format for modeling and analysis.

The dataset developed for this study covers the Kachhi Plain Basin, which includes the Nari, Bolan, and Mula Rivers, where no gauging stations are available to provide observed discharge records. Daily precipitation data were obtained from the ERA5 reanalysis product at a spatial resolution of 25 km for the period 2011–2022.

Catchment characteristics were derived from multiple sources: land use and land cover information were extracted from the ESRI Land Use/Land Cover dataset, soil properties were obtained from the FAO soil database, and watershed topography was defined using the USGS digital elevation model (DEM).

These datasets were integrated within the HEC-HMS hydrological model to simulate daily runoff at the basin outlet. The simulated runoff was initially produced in units of mm³/day and was subsequently converted into m³/s to align with standard hydrological practice. Since the basin lacks direct discharge observations, this HEC-HMS simulated runoff served as the proxy observed dataset for further analysis.

Note: This dataset is freely accessible for educational and research purposes only. Users who employ are requested to reference/cite this dataset with proper acknowledgement and cite the corresponding DOI (10.5281/zenodo.17302968) in their publications/reports etc.
DOI: 10.6075/j0rn36z0
title: CIL:12957, Rattus rattus, glandular epithelial cell, milk secreting cell, mammary alveolar cell. In Cell Image Library

description: Immunoelectron microscopy of mammary gland tissue from lactating rats investigating potential structural interactions between mature lipid droplets and elements of the trans-Golgi network, identified by TGN38 (a transmembrane trans-Golgi protein; larger gold particles) and GOLPH3 (a trans-Golgi associated protein that can also be associated with mitochondria; smaller gold particles) staining. Note that trans‐Golgi cisternae in lactating mammary cells contain large amounts of casein and other milk proteins and are grossly expanded due to the osmolarity of the secreted fluid.
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); illumination by electrons; detection of electrons
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;intensitiesquantitation
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 sequential incubation with antibodies to GOLPH3 (rabbit polyclonal GMx33) and TGN38 (mouse monoclonal 2F7) and colloidal gold-conjugated secondary antibodies (10 nm anti-rabbit, 15 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. Magnification 21,000 X. See Ladinsky and Howell (2007) for more information on methods used.
DOI: 10.6075/j0q2408r
title: CIL:12435, Rattus, multipolar neuron. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dissociated postmitotic neuron grown 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
description: Presynaptic contacts are abundant on both cell bodies and the dendritic arbor of cultured hippocampal neurons after 15 days in vitro. Neurons were immunostained for MAP2, a microtubule associated protein localized to dendrites (green) and synapsin I (red), a presynaptic vesicle protein. With the exception of the immunostained presynaptic terminals, axons are not visible in this preparation. A relatively low power objective (20X) was used to capture the entire dendritic arbor of individual cells.
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 MAP2 (monoclonal HM2, Sigma, with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and synapsin I (from P. DeCamilli, with DyLight549 conjugated secondary, excitation, 555, emission, 568, [Jackson Immunoresearch]). Images were acquired with a Leica DMRA microscope with a 20X (HC Fluotar, NA 0.5) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. Individual images of each fluorophore were colorized and assembled as a a stack file using MetaMorph software.
DOI: 10.6075/j0930scq
title: CIL:2250, Caenorhabditis elegans. In Cell Image Library

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: 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: 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 6 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/j0w37v10
title: CIL:7621, Rattus rattus, epithelial cell, intestinal epithelial cell. In Cell Image Library

description: Preparation: osmium tetroxide fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM); illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: lead salt
Processing history: digitized lantern slide
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
description: Fixative was injected into the intestinal lumen of a rat (3% osmium tetroxide buffered at pH 7.6 with acetate- veronal). Tissue may have also been fixed in potassium permanganate. Tissue blocks were embedded in Epon. Sections were stained with lead hydroxide. Micrograph was taken at original magnification of 96,000 X with a Siemens Elmiskop I, operating at 60 or 80 kv, with a double condenser, and a 50 µ objective aperture. Digitization process: conversion from a 1200 dpi tiff, 3820 x 3342 pixels. Original image created on January 5, 1962. Original resource provided as a 3.25 x 4 inch lantern slide. Research conducted at The Rockefeller Institute of Medical Research (New York, NY).
description: Junctional complex between two cells in the epithelium of the rat intestinal mucosa. The tight junction (also known as zonula occludens, ZO) located nearest to the lumen extends from arrow 1 to arrow 2. The elimination of the intercellular gap (approx 90 angstroms) is clearly visible, but the fusion line of the two apposed membranes cannot be clearly distinguished at this magnification. The adherens junction (also known as zonula adherens, ZA) extends from arrow 3 to arrow 4. A relatively wide intercellular space (approx 200 angstroms) is maintained throughout this junction. Extensive actin filament networks are seen along both sides of the junction (Actin) which are continuous with the terminal web (TW) into which the filamentous rootlets of the mircovilli penetrate. Dense material (DM) can be seen along parts of both sides of the junction. The limits of a desmosome are marked by arrows 5 and 6. Desmosomes are characterized by a wide intracellular space (approx 240 angstroms) bisected by an intermediate line (id). Bundles of intermediate filaments (if, diameter approx 80 angstroms) converge into a dense plaque (DP) on each side of the desmosome. The trilaminar structure of the cell membrane (CM) is clearly seen along the microvilli (MV), between the ZA and the desmosome and within the desmosome. First description of 1) tight junctions and 2) the junctional complexes between epithelial cells, consisting of tight junction, adherens junction and a desmosome. Identical unlabeled image available as CIL# 7620. Image published as Figure 1 in Farquhar and Palade, 1963.
DOI: 10.6075/j08p5zgk
title: CIL:36511, Xenopus laevis, fertilized egg. In Cell Image Library

description: Images collected on a Zeiss LSM 710 confocal with a 10X 0.3 NA objective using 561 and 633 laser lines.
description: This image is part of a large data set of Xenopus laevis eggs imaged at various times post fertilization (the first number of the file name corresponds minutes, eg 30_2 is 30 min post fertilization). The embryos are stained for alpha-tubulin (green) using a directly labeled B-5-1-2 antibody and DNA (red).
description: Preparation: methanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; distribution of a specific protein
Visualization methods: labeled primary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0222sts
title: CIL:8044, Mus musculus. In Cell Image Library

description: Fluorescence recovery after photobleaching (FRAP)kinetics of MeCP2 were recorded using a mouse fibroblast cell line stably expressing MeCP2-GFP. Live cells were imaged using a Zeiss LSM 510 meta confocal microscope with fluorescence excitation at 488 nm and a 63x plan-apo oil lens. The image series has 2 pre-bleach shots, one immediately after bleaching two 1 micrometer diameter circles of pericentromeric heterochromatin, followed by 105 images at 2 sec intervals.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: quantity of GFP-protein
Visualization methods: Green fluorescent proteins from Anthozoa
Processing history: unprocessed raw data
DOI: 10.6075/j0mc903k
title: CIL:35804, 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 MCM1. 
 
 MCM1 is a transcription factor involved in cell-type-specific transcription and pheromone response; plays a central role in the formation of both repressor and activator complexes
 
These phase,gfp images are part of an image group that ranges from CIL:35880-35899. 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 photons
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/j0ht2nkm
title: CIL:1017, Caenorhabditis elegans, muscle cell. In Cell Image Library

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: 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: 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/j0xp751w
title: CIL:10264, Rattus, multipolar neuron. In Cell Image Library

description: Early stages of dendritic development and synapse formation in cultured hippocampal neurons. This multilayer image shows neurons fixed at 7 days in vitro and immunostained for the dendritically localized protein MAP2 (green) and the presynaptic vesicle protein Synapsin I (red). Unstained axons in the field are evident in the phase channel, which is hidden but can be turned on in the viewer. Neurons at 3, 5 and 7 days in vitro are represented in this image group. 

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, warmed to 37°C prior to fixation, 15 minutes), permeabilized with 0.25% Triton (7 minutes) and immunostained for MAP2 (monoclonal HM2, Sigma, with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and synapsin I (from P. DeCamilli, with DyLight549 conjugated secondary, excitation, 555, emission, 568, [Jackson Immunoresearch]). Images were acquired with a Leica DMRA microscope with a mercury arc lamp, a 40X lens (HCX PL Fluotar, NA 0.75), Leica GFP filter set (excitation, BP 470/40; dichromatic mirror, 500; suppression filter, BP 525/50); Leica N3 filter set (excitation, BP546/12; dichromatic mirror, 565, suppression filter, BP 600/40), Photometrics CoolSnap ES CCD camera and MetaMorph software.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
DOI: 10.6075/j0d50m5k
title: CIL:1115, Caenorhabditis elegans, muscle cell. In Cell Image Library

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 4 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.
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
DOI: 10.6075/j0jw8dk0
title: CIL: 53611, Homo sapiens, HeLa. In Cell Image Library

description: Atypical 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: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
description: Visualization methods: confocal microscopy
DOI: 10.6075/j0gm862d
title: CIL:12663, Danio rerio. In Cell Image Library

description: High magnification scanning EM of the extracellular matrix in the ventrolateral mesoderm of a 24 hr (prim-5) Zebrafish embryo. Specimens were chemically fixed critically point dried, and sputter coated with gold/palladium. This image is part of a series taken by Bryan Crawford while he was at the University of Washington. They are part of the Zebrafish--The Living Laboratory CD made available by Mark Cooper and described in Methods in Cell Biology Volume 77, 2004, Pages 439-457. These images were taken by Bryan Crawford while he was at the University of Washington. They are part of the Zebrafish--The Living Laboratory CD made available by Mark Cooper and described in Methods in Cell Biology Volume 77, 2004, Pages 439-457.
description: Preparation: crosslinking-fixative fixed tissue; critical_point dried specimen
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements