cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0571b72
title: CIL:1946, Caenorhabditis elegans. In Cell Image Library

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 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: 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
DOI: 10.6075/j02b8wwz
title: CIL:41640, Montastraea annularis, symbiodinium, polyps. In Cell Image Library

description: Underwater image of live coral Montastraea annularis. Note polyp tissue (green) around the mouth and base of the tentacles and zooxanthellae or symbiodinium (red fluorescence from chlorophyll) in the tissue between polyps. Tentacles also are visible. Fluorescence microscopy. Honorable Mention, 2011 Olympus BioScapes Digital Imaging Competition©.
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: autofluorescence
DOI: 10.6075/j0rn36pd
title: CIL:40986, Paramecium. In Cell Image Library

description: Phase contrast movie demonstrating how paramecia contractile vacuoles regulate water pressure within the protozoan's body. Water enters through the cell wall by osmosis and then passes through the cytoplasm to the vacuole's canals. When filled, the vacuole expels the water from the cell's body. This movie won Fourth Prize, 2011 Olympus BioScapes Digital Imaging Competition©.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
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
DOI: 10.6075/j02j6b8k
title: CIL: 51276, 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.
DOI: 10.6075/j0pn94xc
title: CIL:707, Necturus maculosus, nucleate erythrocyte. In Cell Image Library

description: Preparation: unembedded tissue; glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: elastic scattering
Visualization methods: other negative stain
Processing history: raw unprocessed data
description: X-ray analysis shows that the nucleated erythrocytes of the amphibian Necturus maculosus (Mud Puppy) contains more ordered chromatin than most nuclei. Here, chromatin fibers were isolated from N. maculosus erythrocyte nuclei using mild micrococcal nuclease digestion, fixed briefly with glutaraldehyde, applied to thin carbon films and negatively stained with methylamine tungstate. ~30 nm fibers are seen, some exhibiting short regions with apparent structural order.
DOI: 10.6075/j0jh3kb7
title: CIL:18451, damselfly, flight muscle cell. In Cell Image Library

description: Most images show fractures through the outer membrane of mitochondria and SR/T tubules of dyads nestled in long grooves of the mitochondrial surface. All leaflets of the membranes appear in the images. This image is part of the group image CFA00512. TEM magnifications is not available for this image. The negative film was scanned at LBL then reduced in size for upload. Scan step size is 6.3 micron, then reduced in size 4X for upload, for an effective pixel size of 25 micron. Technical details: Heads and tail removed, thorax bisected and immersed in 3% glutaraldehyde buffered in 0.1 M cacodylate buffer. pH 7.2. stored at 4C for several days. Muscle dissected out. Infiltrated in 30% glycerol in water. Frozen in liquid nitrogen cooled Freon, fractured in Balzers 400 Freeze-fracture, shadowed with platinum at 45o angle. Replicas were cleaned with Clorox (to remove tissue and with either sulfuric acid or NaOH to try removing the tracheolae. Replicas examined in a Philips 410 Microscope. Reference for these images: 
Takekura, H. and Franzini-Armstrong C. The structure of Ca2+ release units in arthropod body muscle indicates an indirect mechanism for excitation-contraction coupling. Biophys. J. 83, 83, 2742-2753, 2002.
description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: unembedded tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: digitized negative film
Data qualification: Raw
DOI: 10.5281/zenodo.17489962
title: An Open-access Database for the Evaluation of Cardio-mechanical Signals from Patients with Valvular Heart Diseases

description: This dataset is for the paper "An Open-access Database for the Evaluation of Cardio-mechanical Signals from Patients with Valvular Heart Diseases" published to Frontiers in Physiology. Please cite "Yang C, Fan F, Aranoff N, Green P, Li Y, Liu C and Tavassolian N (2021) An Open-Access Database for the Evaluation of Cardio-Mechanical Signals From Patients With Valvular Heart Diseases.Front. Physiol. 12:750221. doi: 10.3389/fphys.2021.750221" when using this database.

The archive comprises SCG and GCG recordings sourced from and processed at multiple sites worldwide, including Columbia University Medical Center and Stevens Institute of Technology in the USA, as well as Southeast University, Nanjing Medical University, and the first affiliated hospital of Nanjing Medical University in China. It includes electrocardiogram (ECG), SCG, and GCG recordings collected from 100 patients with various conditions of valvular heart diseases, such as aortic and mitral stenosis. The recordings were collected from clinical environments with the same types of wearable sensor patch. Besides the raw recordings of ECG, SCG and GCG signals, a set of hand-corrected fiducial point annotations is provided by manually checking the results of the annotated algorithm. The database also includes relevant echocardiogram parameters associated with each subject such as ejection fraction, valve area, and mean gradient pressure.

Version 1.1 change log:

Upload the missing MATLAB script files. "Mat_Convert_CP.m" and "Mat_Convert_UP.m"
description: The work in China is supported by the Distinguished Young Scholars of Jiangsu Province (BK20190014), the National Natural Science Foundation of China (62101120, 62001111 and 81871444), and the Primary Research & Development Plan of Jiangsu Province (BK20210208, BK20200364 and BE2017735). The data collection and processing in the USA are funded by National Science Foundation (NSF) under award number 1855394.
DOI: 10.5281/zenodo.5279447
title: An Open-access Database for the Evaluation of Cardio-mechanical Signals from Patients with Valvular Heart Diseases

description: This dataset is for the paper "An Open-access Database for the Evaluation of Cardio-mechanical Signals from Patients with Valvular Heart Diseases" published to Frontiers in Physiology. Please cite "Yang C, Fan F, Aranoff N, Green P, Li Y, Liu C and Tavassolian N (2021) An Open-Access Database for the Evaluation of Cardio-Mechanical Signals From Patients With Valvular Heart Diseases.Front. Physiol. 12:750221. doi: 10.3389/fphys.2021.750221" when using this database.

The archive comprises SCG and GCG recordings sourced from and processed at multiple sites worldwide, including Columbia University Medical Center and Stevens Institute of Technology in the USA, as well as Southeast University, Nanjing Medical University, and the first affiliated hospital of Nanjing Medical University in China. It includes electrocardiogram (ECG), SCG, and GCG recordings collected from 100 patients with various conditions of valvular heart diseases, such as aortic and mitral stenosis. The recordings were collected from clinical environments with the same types of wearable sensor patch. Besides the raw recordings of ECG, SCG and GCG signals, a set of hand-corrected fiducial point annotations is provided by manually checking the results of the annotated algorithm. The database also includes relevant echocardiogram parameters associated with each subject such as ejection fraction, valve area, and mean gradient pressure.

Version 1.1 change log:

Upload the missing MATLAB script files. "Mat_Convert_CP.m" and "Mat_Convert_UP.m"
description: The work in China is supported by the Distinguished Young Scholars of Jiangsu Province (BK20190014), the National Natural Science Foundation of China (62101120, 62001111 and 81871444), and the Primary Research & Development Plan of Jiangsu Province (BK20210208, BK20200364 and BE2017735). The data collection and processing in the USA are funded by National Science Foundation (NSF) under award number 1855394.
DOI: 10.6075/j0br8rp7
title: CIL: 52269, 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=2, y=5, z=13 from BL_024216_Myc_Terc
DOI: 10.6075/j0c827wx
title: CIL:46052, Homo sapiens. In Cell Image Library

description: Plate 26640 - 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/j0j9652r
title: CIL:36282, Vorticella convallaria, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Modified basal bodies, composed of a circle of 9 single microtubules, occur along the length of the stalk and these basal bodies lie against the alveolar-bearing side of the stalk. Fibers pass into these basal bodies from the ER linkage complexes of mid pieces in the spasmoneme. TEM taken on 2/23/72 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 23,500X. Bar = 0.2µm.Published and adapted with permission from J. Cell Biol. 56:559-579, 1973. 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:39510) 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: 10.6075/j0cf9p1g
title: CIL:35482, Homo sapiens, hepatocyte. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; formaldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of nucleic acids
Visualization methods: propidium iodide
Processing history: unprocessed raw data
Data qualification: Processed
description: HuH-7 cells are an immortalized cultured cell line derived from hepatic carcinoma. Cells were grown on 1.5 glass coverslips, fixed with formaldehyde and glutareldehyde, extracted, and labeled for fluorescence microscopy with commercial antibodies to alpha- or beta-tubulin and propidium iodide. The coverslip was mounted on a slide in PBS and glycerol with n-propyl gallate as an antifading agent. Imaging was performed with a BioRad MRC 600 laser scanning confocal microscope with a Kr/Ar laser with lines at 488 and 568 nm. The microscope was a fixed tube length Nikon Diaphot with 60X N.A. 1.4 phase 3 optics. Z series was collected at 0.2 um step sizes. The original XY spatial scale has been lost.
description: Tripolar mitosis in a liver cancer cell line. Normally, dividing cells form a single metaphase plate of paired chromosomes which are pulled apart by opposing microtubule spindles. The Z series, obtained with a laser scanning confocal microscop,e shows abnormal division by mis-segregated chromosomes.
 This image group includes other z-series and a 3D surface representation
DOI: 10.6075/j0td9w6w
title: CIL:38812, blood cell. In Cell Image Library

description: Image B0006427 Scanning electron micrograph 2006 Collection: Wellcome Images Copyrighted work available under Creative Commons by-nc-nd 2.0 UK: England & Wales, see http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
description: Preparation: chemically fixed tissue
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: visualization of contiguous regions
Processing history: colorized
description: Color-enhanced scanning electron micrograph of red blood cells leaking out of a ruptured blood vessel. This is due to a mutation in the ephrin-B2 gene that causes the blood vessels to be more fragile than normal leading to an increased rate of haemorrhaging. The fragility is due to the inadequate coverage of the vessel by smooth muscle cells. This kind of leaky blood vessel is frequently found in tumours and in certain other human diseases.
DOI: 10.6075/j0tx3f7v
title: CIL:36937, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

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: 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: This is IMAGE #1 (day 1) 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: 10.6075/j0v98741
title: CIL:2579, 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 10 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.