cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j01r6pj2
title: CIL:7115, Homo sapiens, neuron. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: microscopy; atomic force microscopy
Parameter imaged: specimen height
Source of contrast: specimen height
Processing history: unprocessed raw data
description: The protein MeCP2 binds to symmetrically methylated CpG dinucleotides and is thought to transmit the (generally) repressive signals encoded in DNA methylation patterns. Mutations in MeCP2 lead to Rett syndrome. Here, MeCP2-DNA complexes have been imaged by AFM (Digital Instruments Nanoscope) in air using human MeCP2 and an 828 bp DNA sequence containing several methylated CpGs. MeCP2 molecules appear as bright particles in AFM images. Volume measurements of the complexes suggest that MeCP2 monomers (circular particles) and dimers (larger elliptical particles) are present and suggest that MeCP2 binds DNA cooperatively. Other images in the grouped set show looped structures and large complexes containing multiple DNA strands and MeCP2 molecules. These configurations are likely promoted by the multiple independent DNA-binding domains of MeCP2 and relevant to the in vivo interactions between MeCP2 and chromatin.
DOI: 10.6075/j03777p9
title: CIL:7114, Homo sapiens, neuron. In Cell Image Library

description: The protein MeCP2 binds to symmetrically methylated CpG dinucleotides and is thought to transmit the (generally) repressive signals encoded in DNA methylation patterns. Mutations in MeCP2 lead to Rett syndrome. Here, MeCP2-DNA complexes have been imaged by AFM (Digital Instruments Nanoscope) in air using human MeCP2 and an 828 bp DNA sequence containing several methylated CpGs. MeCP2 molecules appear as bright particles in AFM images. Volume measurements of the complexes suggest that MeCP2 monomers (circular particles) and dimers (larger elliptical particles) are present and suggest that MeCP2 binds DNA cooperatively. Other images in the grouped set show looped structures and large complexes containing multiple DNA strands and MeCP2 molecules. These configurations are likely promoted by the multiple independent DNA-binding domains of MeCP2 and relevant to the in vivo interactions between MeCP2 and chromatin.
description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: microscopy; atomic force microscopy
Parameter imaged: specimen height
Source of contrast: specimen height
Processing history: unprocessed raw data
DOI: 10.6075/j0pz582d
title: CIL:721, Chlorocebus sabaeus. In Cell Image Library

description: COS 7 cell expressing Organelle LightsTM ER-GFP (Invitrogen) consiting of the signal sequence of the ER protein calreticulin and a KDEL
retention sequence. Images were collected with a 63X 1.4 NA Plan-Apochromat oil objective on a Zeiss LSM510 META (Carl Zeiss,Thornwood, NY) using 488 nm excitation, HFT 488 dichroic, and LP505 emission filter. Image size is 1024 x 1024, pixel size is 0.07 µm x 0.07 µm and pixel time was set to 1.28 ¬µsec. Detector pinhole was set to collect 25 ~0.5 µm slices at 0.5 µm intervals.
description: Preparation: living tissue
Relation to intact cell: living tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: UV/visible/IR photons
Visualization methods: EGFP
DOI: 10.6075/j0fb51zs
title: CIL:7121, Homo sapiens, neuron. In Cell Image Library

description: The protein MeCP2 binds to symmetrically methylated CpG dinucleotides and is thought to transmit the (generally) repressive signals encoded in DNA methylation patterns. Mutations in MeCP2 lead to Rett syndrome. Here, MeCP2-DNA complexes have been imaged by AFM (Digital Instruments Nanoscope) in air using human MeCP2 and an 828 bp DNA sequence containing several methylated CpGs. MeCP2 molecules appear as bright particles in AFM images. Volume measurements of the complexes suggest that MeCP2 monomers (circular particles) and dimers (larger elliptical particles) are present and suggest that MeCP2 binds DNA cooperatively. Other images in the grouped set show looped structures and large complexes containing multiple DNA strands and MeCP2 molecules. These configurations are likely promoted by the multiple independent DNA-binding domains of MeCP2 and relevant to the in vivo interactions between MeCP2 and chromatin.
description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: microscopy; atomic force microscopy
Parameter imaged: specimen height
Source of contrast: specimen height
Processing history: unprocessed raw data
DOI: 10.5517/ccdc.csd.cc2l7sl7
title: CCDC 2390769: Experimental Crystal Structure Determination

description: Related Article: Giuseppe Pileio, Dolnapa Yamano, Craig Eccles, Graham J. Tizzard, Sam Thompson|2025|CSD Communication|||
description: Related Article: Giuseppe Pileio, Dolnapa Yamano, Craig D. Eccles, Graham J. Tizzard, Sam Thompson
|2025|Frontiers in Chemistry|12|1511720|doi:10.3389/fchem.2024.1511720
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6075/j0jd4w35
title: CIL:712, Necturus maculosus, nucleate erythrocyte. In Cell Image Library

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.
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
DOI: 10.6075/j0rj4hjp
title: CIL:7118, Homo sapiens, neuron. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: microscopy; atomic force microscopy
Parameter imaged: specimen height
Source of contrast: specimen height
Processing history: unprocessed raw data
description: The protein MeCP2 binds to symmetrically methylated CpG dinucleotides and is thought to transmit the (generally) repressive signals encoded in DNA methylation patterns. Mutations in MeCP2 lead to Rett syndrome. Here, MeCP2-DNA complexes have been imaged by AFM (Digital Instruments Nanoscope) in air using human MeCP2 and an 828 bp DNA sequence containing several methylated CpGs. MeCP2 molecules appear as bright particles in AFM images. Volume measurements of the complexes suggest that MeCP2 monomers (circular particles) and dimers (larger elliptical particles) are present and suggest that MeCP2 binds DNA cooperatively. Other images in the grouped set show looped structures and large complexes containing multiple DNA strands and MeCP2 molecules. These configurations are likely promoted by the multiple independent DNA-binding domains of MeCP2 and relevant to the in vivo interactions between MeCP2 and chromatin.
DOI: 10.6075/j0dv1hw1
title: CIL:7242, Homo sapiens, epithelial cell. In Cell Image Library

description: HeLa cells at last stage of cytokinesis were fixed and stained with microtubules (green), PRC1 (red), and KIF4A (blue). PRC1 and KIF4A colocalized on midbody in the center of intracellular bridge and a dark zone which cannot be accessed by antibodies was shown.

Cells were fixed with MeOH on ice for 3 min, and stained with primary antibodies against PRC1 (Protein regulator of cytokinesis 1), KIF4A (Chromosome-associated kinesin), and FITC-DM1a antibody against microtubules. Secondary antibodies were Alexa 594 for PRC1, and Alexa 647 for KIF4A. A single section was collected with a spinning disk microscope on a Nikon TE-2000 with a 1.3 NA 100X objective. Images were collected with an OrCA ER CCD camera.
Lasers and filters: Innova 70C Spectrum 3 watt Laser, 488 Laser/ATOF 525/50, 568 Laser/ATOF 605/52, and 647 Laser ATOF 700/75.
description: Preparation: methanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: labeled primary antibody; primary antibody plus labeled secondary antibody; Alexa Fluor 594; Alexa Fluor 647
Processing history: unprocessed raw data
DOI: 10.6075/j0hh6j4z
title: CIL:7319, Halteria grandinella, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

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; unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: High resolution image of the buccal cavity of Halteria has oral ciliature on its left side and a paroral kinety consisting of only one row of basal bodies and cilia on its right side. A cytopharynx with microtubular lamellae arises to the right of the paroral kinety where it will continue deep into the cell as a cytopharyngeal tube accompanied by the microtubular lamellae. A thick layer of microtubules covers one side of the buccal cavity. Mitochondria are both expanded and condensed). TEM taken on 3/12/71 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 9,250X. The raw film was scanned with a Nikon Coolscan 9000ED. This image is suitable for quantitative analysis.

Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness.

Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0833r23
title: CIL:7241, Homo sapiens, epithelial cell. In Cell Image Library

description: HeLa cells at last stage of cytokinesis were fixed and stained with microtubules (green), PRC1 (red), and KIF4A (blue). PRC1 and KIF4A colocalized on midbody in the center of intracellular bridge and a dark zone which cannot be accessed by antibodies was shown.

Cells were fixed with MeOH on ice for 3 min, and stained with primary antibodies against PRC1 (Protein regulator of cytokinesis 1), KIF4A (Chromosome-associated kinesin), and FITC-DM1a antibody against microtubules. Secondary antibodies were Alexa 594 for PRC1, and Alexa 647 for KIF4A. A single section was collected with a spinning disk microscope on a Nikon TE-2000 with a 1.3 NA 100X objective. Images were collected with an OrCA ER CCD camera.
Lasers and filters: Innova 70C Spectrum 3 watt Laser, 488 Laser/ATOF 525/50, 568 Laser/ATOF 605/52, and 647 Laser ATOF 700/75.
description: Preparation: methanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: labeled primary antibody; primary antibody plus labeled secondary antibody; Alexa Fluor 594; Alexa Fluor 647
Processing history: unprocessed raw data
DOI: 10.6075/j0f76bsm
title: CIL:724, Chlorocebus sabaeus. In Cell Image Library

description: COS 7 cell expressing Organelle LightsTM PM-GFP (Invitrogen)consisting of the myristoylation/palmitoylation sequence from Lck
tyrosine kinase. Images were collected with a 63X 1.4 NA Plan-Apochromat oil objective on a Zeiss LSM510 META (Carl Zeiss,Thornwood, NY) using 488 nm excitation, HFT 488 dichroic, and LP505emission filter. Image size is 1024 x 1024, pixel size is 0.14 µm x 0.14 µm and pixel time was set to 1.6 ¬µsec. Detector pinhole was set to collect ~0.5 µm slices at 0.5 µm intervals
description: Preparation: living tissue
Relation to intact cell: living tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: UV/visible/IR photons
Visualization methods: EGFP
DOI: 10.6075/j0vx0fj2
title: CIL:7224, Homo sapiens, epithelial cell. In Cell Image Library

description: Preparation: methanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: primary antibody plus labeled secondary antibody; Alexa Fluor 594; Fluorescein (FITC); labeled primary antibody
Processing history: unprocessed raw data
description: Distribution of Golgi Apparatus during cell division. Hela cells fixed with MeOH on ice for 3 min, and stained with a primary antibody against the Golgi and FITC conjugated DM1a antibody (green) against microtubules. Secondary antibody was Alexa 594 for the Golgi (red). A single section was collected with a spinning disk microscope on a Nikon TE-2000 with a 1.3 NA 100X objective. Images were collected with an Orca ER CCD camera.
Lasers and filters: Innova 70C Spectrum 3 watt Laser, 488 Laser/ATOF 525/50, and 568 Laser/ATOF 605/52.
DOI: 10.6075/j0f47nf6
title: CIL:722, Chlorocebus sabaeus. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: living tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: UV/visible/IR photons
Visualization methods: EGFP
description: COS 7 cell expressing Organelle LightsTM ER-GFP (Invitrogen) consisting of the signal sequence of the ER protein calreticulin and a KDEL
retention sequence. Images were collected with a 63X 1.4 NA Plan-Apochromat oil objective on a Zeiss LSM510 META (Carl Zeiss,Thornwood, NY) using 488 nm excitation, HFT 488 dichroic, and LP505emission filter. Image size is 1024 x 1024, pixel size is 0.07 µm x 0.07 µm and pixel time was set to 1.28 ¬µsec. Detector pinhole was set to collect 25 ~0.5 µm slices at 0.5 µm intervals.
DOI: 10.6075/j0sn081w
title: CIL:7199, Mammalian Cell Animation. In Cell Image Library

description: Relation to intact cell: microtome-sectioned tissue; whole mounted cell; animation
Item type: transmission electron microscopy (TEM); confocal microscopy; TEM tomography
Imaging mode: SEM animation
description: The Golgi Apparatus. In mammalian cells, the very complex architecture of the membrane system makes understanding the interrelationship of the different organelles within the cell difficult. Their dynamic relationship exists in four dimensions and is hard to capture at nanoscale resolutions. We present, here, an animation that takes the viewer inside a mammalian cell where one can see the nucleus and its characteristic envelope connected to the endoplasmic reticulum. We used transmission electron microscopy and tomography to generate a 3D volume of a portion of a Golgi ribbon imaged from a mammalian cell. A model of the Golgi apparatus is presented where the trans Golgi network peels off from the stack of cisternae while the CIS element is fed with a component arising from the ER exit site. This animation is the first project by the Biovisualization program at the NICHD. Computer science and animation students collaborated with researchers to produce this visualization. While the main focus was scientific accuracy, aesthetics were also considered. To convey the sense of scale, a progression is made, from actual confocal microscopy into an SEM style animation and then into non-photorealistic rendering of what can be seen at TEM level magnification. The software tools utilized for this project include Autodesk Maya, Adobe Photoshop and After Effects, Final Cut Studio, Mercury Amira and Imod. Title: Celldance 2008, 1st Place Public Outreach Video: The Golgi Apparatus
DOI: 10.6075/j0r210f5
title: CIL:7239, Homo sapiens, epithelial cell. In Cell Image Library

description: HeLa cells were accumulated in monopolar mitosis using a 12 hr treatment of the kinesin-5 inhibitor S-trityl-l-cysteine and forced into cytokinesis by adding the potent Cdk1 inhibitor purvalanol A for 15 min. The microtubules (green) were not growing and shrinking. Aurora B (red), which functions in attaching microtubules to the centromere, localizes at the gap region between the cortex and the microtubule plus ends.

Cells were fixed with MeOH on ice for 3 min, and stained with a primary antibody against Auruoa B and FITC-DM1a antibody against microtubules. Secondary antibody was Alexa 594 for Aurora B. A single section was collected with a spinning disk microscope on a Nikon TE-2000 with a 1.3 NA 100X objective. Images were collected with an Orca ER CCD camera.
Lasers and filters: Innova 70C Spectrum 3 watt Laser, 488 Laser/ATOF 525/50, and 568 Laser/ATOF 605/52.
description: Preparation: methanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: primary antibody plus labeled secondary antibody; Fluorescein (FITC); Alexa Fluor 594; labeled primary antibody
Processing history: unprocessed raw data
DOI: 10.6075/j0959gsg
title: CIL:726, Chlorocebus sabaeus. In Cell Image Library

description: COS 7 cell expressing Organelle LightsTM PM-GFP (Invitrogen)consisting of the myristoylation/palmitoylation sequence from Lck
tyrosine kinase. Images were collected with a 63X 1.4 NA Plan-Apochromat oil objective on a Zeiss LSM510 META (Carl Zeiss,Thornwood, NY) using 488 nm excitation, HFT 488 dichroic, and LP505emission filter. Image size is 1024 x 1024, pixel size is 0.14 µm x 0.14 µm and pixel time was set to 1.6 ¬µsec. Detector pinhole was set to collect 29 ~0.5 µm slices at 0.5 µm intervals.
description: Preparation: living tissue
Relation to intact cell: living tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: UV/visible/IR photons
Visualization methods: EGFP
DOI: 10.15468/dl.fmz6zu
title: Occurrence Download

description: A dataset containing 322827 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Pinus pinea"
 ]
}

 The dataset includes 322827 records from 438 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009704-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0k64h5r
title: CIL:7248, mouse/rat NG108-15. In Cell Image Library

description: Preparation: unfixed tissue
Relation to intact cell: living tissue
Item type: recorded image
Imaging mode: slit-scan confocal
Parameter imaged: fluorescence emission
Source of contrast: UV/visible/IR photons
Visualization methods: EGFP
Processing history: unprocessed raw data
description: NG108-15 cells expressing EGFP-actin. NG108-15 cells are a cell line that is derived from a mouse neuroblastoma and a rat glioma. This is one of two images related images that show actin dynamics in the growth cones of the NG108 cells. This image captures the actin dynamics of multiple processes on the NG108 and the related image shows a more detailed view of filopodial dynamics in the growth cone.

Images were collected as a single z slice time series on a Carl Zeiss 5 LIVE microscope. The Zeiss 5 LIVE uses a cylindrical lense to create a sheet of illumination that is rapidly scanned in the vertical direction and detected on a linear CCD array to enable faster imaging. The images were collected with a 63X 1.4 NA plan apo objective. Filers: NFT 490 and BP 500-525. 28 micron slit width. Pixel dwell 972 micros yielded approximately 2 frames collected per s.
DOI: 10.5281/zenodo.17493383
title: Photomask linewidth measurement comparison including an improved model-based through-focus measurement approach

description: The here provided data includes the measured focus series of varrying iso and dense trench and line features on the nanoacale. The data was used for the evaluation of optical bidirectional measuremetns for all features. The results are provided in the submitted publication with the same title as above.

In total, there are 20 different strucutres. The focus series data is provided in Mat-Files.
DOI: 10.5281/zenodo.17493384
title: Photomask linewidth measurement comparison including an improved model-based through-focus measurement approach

description: The here provided data includes the measured focus series of varrying iso and dense trench and line features on the nanoacale. The data was used for the evaluation of optical bidirectional measuremetns for all features. The results are provided in the submitted publication with the same title as above.

In total, there are 20 different strucutres. The focus series data is provided in Mat-Files.
DOI: 10.6075/j02n51cv
title: CIL:7305, Opercularia [NCBITaxon:168247], Opercularia coarctata, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: High resolution image of the contractile vacuole and the spongiome decorated tubules showing V-type proton pumps extending from the cytosolic side of the tubules; also detail of the micronucleus. TEM taken on 6/10/69 by R. Allen with Philips 300 operating at 60kV. Neg. 14,800X. The raw film was scanned with a Nikon Coolscan 9000ED. This image is suitable for quantitative analysis.

Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness.

Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; unprocessed raw data; raw unprocessed image
Data qualification: Raw;spatialmeasurements;intensitiesquantitation