cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0qv3kz9
title: CIL: 51884, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: A novel cell population analysis to quantify both initial and long-term drug effects, namely pseudopod adaptation and recovery following an initial drug-induced perturbation, adding drug slowly in 1/4 increments over 90 minutes.
description: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
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
DOI: 10.6075/j06q1xbk
title: CIL:10368, Rattus, multipolar neuron. In Cell Image Library

description: Cultured hippocampal neurons after 17 days in vitro, immunostained for MAP2, a microtubule associated protein localized to dendrites (red) but not axons, which are not apparent in the immunofluorescence channel. Both axons, and dendrites, can be seen in the hidden phase micrograph which can be turned on using the edit function in the detailed viewer. Neurons at 10, 14, and 17 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), permeabilized with 0.25% Triton and immunostained for MAP2 (HM2, from Sigma with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 40X lens (HCX PL Fluotar, NA 0.75), Photometrics CoolSnap ES CCD camera and MetaMorph software. A multilayer stack of the fluorescent image of MAP2 staining and the phase image was generated using MetaMorph.
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; elastic scattering of photons
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
DOI: 10.6075/j0p55mg0
title: CIL:7438, Homo sapiens, fibroblast, primary cell line cell. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: Kusabira OrangeFP
Processing history: unprocessed raw data
description: Human foreskin fibroblasts (HFF1) cells transfected with mKusabira-Orange EB3, a marker for growing microtubule ends. Note the dramatic movement of the bright fluorescent markers toward the cell periphery.

Cells were imaged every 3 s by a spinning disk confocal microscoe on a Nikon Ti2000 using a 1.4NA Plan Apo
Ex objective and a solid state 568 laser with a 605x52nm EM filter (Semrock). Images were recorded with a Coolsnap HQ2 (Photometrics) using 500 ms exposures.
DOI: 10.6075/j0ws8s1f
title: CIL:40415, Saccharomyces cerevisiae, CHC1 mutant. In Cell Image Library

description: Transmission electron micrograph of a representative sertraline-treated chc1 mutant cell. CHC1 encodes clathrin heavy chain, which trimerizes to form triskelia that coat vesicles. The vacuolar fragmentation phenotype is reversed by sertraline treatment. (8,000X). The untreated control image for the chc1 mutant is available as CIL 40416.
description: This group of images contains representative whole-cell images and high-magnification zooms of organelle structures of interest. All cells were grown in liquid rich media (YPD pH6.5) at 30C with aerated shaking, and cultures were sampled in mid-logarithmic phase. Treated cells were exposed to 60µM antidepressant sertraline (Zoloft®) for 45 minutes.
description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment
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
Visualization methods: osmium tetroxide
Processing history: unprocessed raw data
DOI: 10.6075/j0251h8z
title: CIL:21743, Drosophila melanogaster, epithelial. In Cell Image Library

description: Five different samples of Drosophila melanogaster Kc167 cells were stained with Hoechst 33342, a DNA stain. The last sample (labeled nodsRNA, CIL 21789) is of wild-type cells. Each of the other four samples (labeled 48, 340, Anillin, and mad2, CIL 21749, 21739, 21759, and 21773, respectively) has a different gene knocked down by RNAi. This is the set that were treated with 340 RNAi. There are 10 images of each sample, for a total of 50 images. The images were acquired on a Zeiss Axiovert 200M microscope. A recommended use for these five image sets is to algorithmically compute the number of cells in each image. A tab-delimited text file containing this information can be found at the URL indicated in the attribution box. The recommended citation when using these images is: "We used the Drosophila Kc167 1 image set (Carpenter, et al., Genome Biology, 2006) available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
description: Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of DNA
Visualization methods: Hoechst 33342
Processing history: unprocessed raw data
DOI: 10.6075/j0tx3d3n
title: CIL:13727, Mus musculus, fibroblast. In Cell Image Library

description: Upon mitochondrial uncoupling, wild-type PINK1-YFP (green) and mCherry-Parkin (red) are localized to mitochondria in PINK1 knock-out mouse embryonic fibroblasts (PINK1 KO MEFs). Transfected PINK1 KO MEFs were treated with the mitochondrial depolarizing agent CCCP (carbonyl cyanide-m-chlorophenyl hydrazone) (10µM) for 3 hours. Live cell imaging was performed on an LSM510 Meta (Carl Zeiss, Inc) with a 63x 1.4 NA oil differential interference contrast Plan Apo objective. Image contrast and brightness were adjusted in the LSM image browser (Zeiss). This image corresponds to Supplemental Figure S1c, bottom left row of J Cell Biol, 191: 933-942, 2010. Images in Supplemental Figure S1c include CIL#s 13725, 13726, 13727, 13728.
description: Preparation: living 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 a specific protein
Visualization methods: EYFP; mCherryFP
Processing history: brightness and contrast adjusted
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.5281/zenodo.17489811
title: O`SMIRLAR VA ULARNING OTA-ONALARIDA KOPING XULQ-ATVORNI NAMOYON BO`LISHINING O`ZIGA XOS XUSUSIYATLARI

description: Mazkur maqolada o‘smirlik davrida koping xulq-atvorni shakllanishiga ta’sir etuvchi shaxs xususiyatlari, xususan ota-onalarning psixologik munosabati va ularning koping strategiyalarining o‘smir farzandlarga ta’siri tahlil qilinadi. Tadqiqotda R. Lazarus va S. Folkman tomonidan ishlab chiqilgan “Koping mexanizmlari” metodikasi qo‘llanildi. Tadqiqot natijalari ota-onalar va o‘smirlarning koping uslublaridagi farqlarni aniqlab, muammoli vaziyatlarga munosabatda shaxsning o‘zini boshqarish, mas’uliyatni qabul qilish va ijobiy qayta baholash strategiyalari muhim omil ekanligini ko‘rsatdi.
DOI: 10.5281/zenodo.17489812
title: O`SMIRLAR VA ULARNING OTA-ONALARIDA KOPING XULQ-ATVORNI NAMOYON BO`LISHINING O`ZIGA XOS XUSUSIYATLARI

description: Mazkur maqolada o‘smirlik davrida koping xulq-atvorni shakllanishiga ta’sir etuvchi shaxs xususiyatlari, xususan ota-onalarning psixologik munosabati va ularning koping strategiyalarining o‘smir farzandlarga ta’siri tahlil qilinadi. Tadqiqotda R. Lazarus va S. Folkman tomonidan ishlab chiqilgan “Koping mexanizmlari” metodikasi qo‘llanildi. Tadqiqot natijalari ota-onalar va o‘smirlarning koping uslublaridagi farqlarni aniqlab, muammoli vaziyatlarga munosabatda shaxsning o‘zini boshqarish, mas’uliyatni qabul qilish va ijobiy qayta baholash strategiyalari muhim omil ekanligini ko‘rsatdi.
DOI: 10.6075/j0c828k9
title: CIL:2272, 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 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.
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/j0qf8s57
title: CIL:1594, 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 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/j0qj7gqb
title: CIL: 51210, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: A novel cell population analysis to quantify both initial and long-term drug effects, namely pseudopod adaptation and recovery following an initial drug-induced perturbation, adding drug slowly in 1/4 increments over 90 minutes.
description: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
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
DOI: 10.6075/j0r210kz
title: CIL:1923, 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 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.
DOI: 10.6075/j0k936t6
title: CIL:40905, uncultured scuticociliate, Conchophthirus curtus, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: shadowing and plating; chemically fixed tissue; lyophilized specimen; Parducz fixative; Au/Pd metal sputter-coat
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: illumination by electrons; secondary_electron imaging
Parameter imaged: illumination by electrons; secondary electron generation; secondary_electron imaging
Source of contrast: detection of electrons
Visualization methods: Deciliation
Processing history: recorded image; film
Data qualification: Raw;spatialmeasurements
description: Conchophthirus was deciliated by calcium ion shock followed by shearing through a micropipette. This revealed the location of the deciliated basal bodies and the cell's surface architecture. In this image of the left side thigmotactic ciliature is revealed at the suture line. Also note that, when zoomed in, in this preparation the clathrin coated pits, which are normally an invagination into the cytoplasm have everted following the deciliation procedure, to form a small evagination anterior to the stubb of each deciliated basal body. For more information see: Antipa, G. A. and Small, E. B. 1971. A redescription of Conchophthirus curtus Engelmann, 1862 (Protozoa, Ciliatea). J. Protozool. 18:491-503. This micrograph was taken in 1968 by G. Antipa on a Cambridge Mark IIA operating at 20kV. The negative magnification is 4420X. The raw film was scanned with an Epson Perfection V750 Pro. This image is available for quantitative analysis.
DOI: 10.15468/dl.vmzc8r
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Juncus inflexus"
 ]
}

 The dataset includes 9 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009217-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0j38rdz
title: CIL:40468, Homo sapiens, osteosarcoma. In Cell Image Library

description: Preparation: chemically fixed tissue; permeabilized tissue
Relation to intact cell: dispersed cells in vitro
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
Processing history: unprocessed raw data
Data qualification: Raw
description: Single slice confocal images representing one optical slice of a cell stained for the Human Protein Atlas (HPA) antibody HPA019493 (shown in green). HPA019493 is a polyclonal anti-LCP-1 antibody that stains the cytoplasm, cell membrane, and actin cytoskeleton. The cells are also stained with reference markers in order to facilitate the annotation of the subcellular distribution of the protein targeted by the HPA antibody. The following probes/organelles are used as references; (i) DAPI for the nucleus (blue) and (ii) anti-tubulin antibody as internal control and marker of microtubules (red).
description: The use of data and images from this site in publications and presentations is permitted provided that the following conditions are met:

The publication and/or presentation are solely for informational and non-commercial purposes.

The source of the data and/or image is referred to this site (www.proteinatlas.org) and/or the above publication is cited.
DOI: 10.6075/j00p0zv4
title: CIL: 54636, Mus musculus, oocyte. In Cell Image Library

description: Oocytes fixed with 2% paraformaldehyde and 1% picric acid. Immunolabelled with anti-Calreticulin (green), Alexafluor 568-phalloidin (red), and Hoechst 33342 (blue).
description: FIG. 4B Changes in cortical ER clusters at the site of sperm binding and incorporation.
description: Imaging mode: whole mount confocal image
Visualization methods: Laser Scan Confocal; PMT
DOI: 10.6075/j09885zn
title: CIL:36751, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; tissue in vitreous ice 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; gold; uranyl salt
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed
description: Glutaraldehyde fixation followed freezing and microtomy. Microtome sections prepared at approximately 75nm thickness. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Phagoacidosomes are heavily labeled for L1 antigen in 5-8 to 15-18 minute-old DVs. However, only some DVs at 15-18 min still had L1 label. Only occasionally did we see tubules with label arising from the 15-18 min-old vacuole to support the idea that DV-II membrane is retrieved during the transformation of phagoacidosomes to phagolysosomes. The DV shown here was 15-18 min old as it contained 0.3µm latex beads. There is a small amount of DV-II specific L1 immunogold label in the tubules and in their bulbous ends. The phagolysosome membrane itself is totally free of this label. TEM taken on 2/18/92 by R. Allen with Zeiss 10A operating at 80kV. Neg. 12,000X. Bar = 0.5µm.
DOI: 10.6075/j0jq10wp
title: CIL: 54810. In Cell Image Library

description: We examined the structural organization of cytoskeletal components and membrane systems in neurons of well preserved biopsy material from Alzheimer’s disease (AD). Information was obtained from thin sectioned material using conventional electron microscopy and from thick sections with the high voltage electron microscope.
description: This image displays degenerating neuron with the cristae junction.
description: Item type: recorded image
Imaging mode: Electronic tomography
DOI: 10.6075/j0kk99g0
title: CIL:35066. In Cell Image Library

description: Preparation: permeabilized tissue; glutaraldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: shadowing and plating; platinum replica
Processing history: unprocessed raw data
description: Procedures for detergent extraction, immunostaining, S1 decoration, light, and EM were described previously (Svitkina et al., 1995, 1996, 1997;Verkhovsky et al., 1995; Svitkina and Borisy, 1998).
description: Electron micrograph of keratocyte or fibroblast lamellipodial actin network after unprotected extraction. All examples demonstrate frequent branching of actin filaments. Image corresponds to a single panel from Figure 2d in J Cell Biol. 1999 May 31;145(5):1009-26. All of the panels from Figure 2d can be found as CIL 35060-35068.