cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0f76bdp
title: CIL:41009, Spirogyra. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: bright-field microscopy; polarized light illumination
Parameter imaged: absorption of illumination; retardance
Source of contrast: differences in intrinsic optical density; intrinsic birefringence
description: Brighfield and polarized light of Spirogyra (a filamentous green algae). Spirogyra is unbranched with cellular cells connected end to end in long green filaments. Sixth Prize, 2010 Olympus BioScapes Digital Imaging Competition©
DOI: 10.6075/j0cv4ghh
title: CIL:40666, Rattus, hippocampal neuron. In Cell Image Library

description: Please refer to referenced article for details on cell extraction and processing for electron microscopy.
description: Preparation: detergent permeabilized; glutaraldehyde fixed tissue; critical_point dried specimen
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
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: colorized
description: Platinum replica illustrating the cytoskeletal organization of dendritic spines from extracted 14 DIV neurons. This image shows branched actin filaments (cyan) in the neck of respective spines.This image is part of a group of images representing Figure 2B and its components from Mol Biol Cell. 2010 Jan 1;21(1):165-76. Figure 2B appears as CIL 40664. The uncolorized overview panel is CIL 40667. Box 4 appears as CIL 40665, and Box 5 (this micrograph) appears as CIL 40666.
DOI: 10.6075/j0rb73z5
title: CIL:40626, Vorticella convallaria, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

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/).
description: The 11 micrographs of the group are views of a serially-sectioned contracted Vorticella convallaria cell that show the main features of this cell. This figure shows 3 food vacuoles; 2 segments of the macronucleus; micronucleus; perioral cilia; tips of ‚Äúribbed wall‚Äù along adoral side of the peristome that contain the lamellae; paroral cilia; contractile vacuole; tube or chamber containing bacteria linking the contractile vacuole to the peristome; and myonemes linking the perioral zone to the cell‚Äôs lateral pellicle. TEM taken on 4/1/71 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 2,150X. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used 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
DOI: 10.6075/j0q52ndp
title: CIL:40562, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: The carrier vesicles dock with the acidosomes and then fuse with these larger vesicles before or as the vesicles dock at the nascent Digestive Vacuole. Thus the contents of the carrier vesicles are first exposed to an acid environment in the acidosomes and phagoacidosomes and then to digestion in the phagolysosomes. (For a discussion of acidosome development see Allen, Ma and Fok, J. Cell Sci. 106:411-422, 1993). TEM taken on 7/19/88 by C. Schroeder with Zeiss 10A operating at 80kV. Neg. 24,800X. Published in J. Cell Sci. 106:411-422, 1993. Adapted with permission.
description: The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0h131cx
title: CIL:40571, Vorticella convallaria, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: The 11 micrographs of the group are views of a serially-sectioned contracted Vorticella convallaria cell that show the main features of this cell. This figure shows the edge of last food vacuole in series; contractile vacuole; bacteria-filled chamber; peristome open to the perioral chamber that opens to the cell‚Äôs exterior. TEM taken on 4/1/71 By R. Allen with Hitachi HU11A operating at 75kV. Neg. 2,650X. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used 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
Data qualification: Raw;spatialmeasurements
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/j0736q7r
title: CIL:40570, Vorticella convallaria, 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
Data qualification: Raw;spatialmeasurements
description: The 11 micrographs of the group are views of a serially-sectioned contracted Vorticella convallaria cell that show the main features of this cell. This figure shows 1 food vacuole; micronucleus; contractile vacuole connected by 2 CV pores to the bacteria-filled chamber; peristome; perikinetids of the perioral cilia. TEM taken on 4/1/71 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 3,400X. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
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/j05t3j8m
title: CIL:40565, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: The tubules arising from late DV-III expand at their distal ends into rounded shapes. These expanded ends contain a glycocalyx like the secondary lysosomes and large IMPs also like secondary lysosomes. TEM taken on 8/7/80 by R. Allen with Hitachi HU11A TEM. Neg. 12,250X. Part published in J. Cell Biol. 99:1955-1959, 1984. Adapted with permission.
description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used 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
DOI: 10.6075/j0xp73tc
title: CIL:40563, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Quick-freeze deep-etch of acidosomes show the results of carrier vesicle fusion with the acidosomes. Both the E-face and P-face of the acidosomes appear to have two areas, the larger area on the E-face has few IMPs but has pits left by the removal of IMPs during fracturing and another area that is smooth with fewer pits that resembles a fused carrier vesicle membrane. A line marking the fusion site between these two vesicles is evident. The P-face of the acidosome has many IMPs while the fused carrier vesicle membrane is smooth. Presumably these two membrane areas will mix with time. Thus acidosomes, which are somewhat similar in appearance to multivesicular bodies in higher organisms, are late endosomes and deliver their membrane, their contents and their V-ATPase complexes to the phagosome to transform the phagosome to the phagoacidosome. TEM taken on 7/29/88 by C. Schroeder with Zeiss 10A operating at 80kV. Neg. 24,800X. Published in J. Cell Sci. 106:411-422, 1993. Adapted with permission.
description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film
Data qualification: Raw;spatialmeasurements
description: The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0gb22xx
title: CIL:40665, Rattus, hippocampal neuron. In Cell Image Library

description: Platinum replica illustrating the cytoskeletal organization of dendritic spines from extracted 14 DIV neurons. Thin spines associate with dendrites at the base (bottom) and with axons by the head (top). This image shows the interaction of actin filaments (cyan) with an axonal microtubule (red).This image is part of a group of images representing Figure 2B and its components from Mol Biol Cell. 2010 Jan 1;21(1):165-76. Figure 2B appears as CIL 40664. The uncolorized overview panel is CIL 40667. Box 4 (this image) appears as CIL 40665, and Box 5 appears as CIL 40666.
description: Preparation: detergent permeabilized; glutaraldehyde fixed tissue; critical_point dried specimen
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
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: colorized
description: Please refer to referenced article for details on cell extraction and processing for electron microscopy.
DOI: 10.6075/j0jh3jzw
title: CIL:40664, Rattus, hippocampal neuron. In Cell Image Library

description: Platinum replica illustrating the cytoskeletal organization of dendritic spines from extracted 14 DIV neurons. Thin spines associate with dendrites at the base (bottom) and with axons by the head (top). Unlabeled insets show the smaller versions of the corresponding main panels with axons color-coded in purple, dendrites in yellow, and spines in cyan. Thick fibers in neurites represent microtubules. Yellow boxes are enlarged in panels with corresponding numbers. Box 4, interaction of actin filaments (cyan) with an axonal microtubule (red). Box 5, branched actin filaments (cyan) in the neck of respective spines.This image is part of a group of images representing Figure 2B and its components from Mol Biol Cell. 2010 Jan 1;21(1):165-76. Figure 2B (this image) appears as CIL 40664. The uncolorized overview panel is CIL 40667. Box 4 appears as CIL 40665, and Box 5 appears as CIL 40666.
description: Preparation: detergent permeabilized; glutaraldehyde fixed tissue; critical_point dried specimen
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
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: colorized
description: Please refer to referenced article for details on cell extraction and processing for electron microscopy.
DOI: 10.6075/j0br8r1q
title: CIL:40661, Rattus, hippocampal neuron. In Cell Image Library

description: Preparation: detergent permeabilized; glutaraldehyde fixed tissue; critical_point dried specimen
Relation to intact cell: dispersed cells in vitro
Item type: grey scale graphic
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: colorized
description: Platinum replica depicting the cytoskeletal organization of dendritic spines in extracted 14 DIV neurons. This image shows the interaction of putative PSD from the spine head with axonal intermediate filaments (green); actin filaments are shown in cyan and a microtubule in red. Image corresponds to Figure 2a in Mol Biol Cell. 2010 Jan 1;21(1):165-76. The entire panel is available as CIL 40660. The uncolorized image is available as CIL 40659. Box 1, (this image) 2, and 3 are CIL 40661, 40662, and 40663, respectively.
description: Please refer to referenced article for details on cell extraction and processing for electron microscopy.
DOI: 10.5281/zenodo.17492056
title: Experimental data, processing and simulation scripts for CHEESY ENDOR

description: Data, processing and simulation scripts for the manuscript: "Resolving spectral overlap in ENDOR by chirp echo Fourier transform detection"All raw data (as .mat files) and MATLAB processing scripts for Figures of the manuscript + SI are supplied. 

For both ScoI and BDPA additional data on chirp echo optimization, excitation transfer function measurements (resonator profiles) and ENDOR nutations is added.

Most processing functions need helper functions to work. These can be found in the folder 'helpers', which is best added to the MATLAB path.

Simulation scripts are found in the 'simulations' folder. The cheesy endor simulation is called 'wasabi' and is called in all other files of the folder to obtain the simulated cheesy endor spectrum.Simulations are based on the EasySpin package, which needs to be in the MATLAB path for the simulations to work.
DOI: 10.6075/j07p8x89
title: CIL:40503, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Quick-freeze deep-etch image of an unfixed and fractured mitochondrion. The tubular cristae average 50nm in diameter. Each cristae bears a helically arranged double row of particles with the particles spaced at 12 nm along this zipper-like arrangement. The cristae themselves assume a helical shape and the zipper array remains on the outside curve of the helix. In in situ fractures the 2 enclosing membranes lie close together. Crystals of unknown composition are often found in the mitochondria. TEM taken on 2/15/88 by C. Schroeder with Zeiss 10A operating at 80kV. Neg. 40,500X. Published in J. Cell Biol. 108:2233-2240, 1989. Adapted with permission. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film
Data qualification: Raw;spatialmeasurements
DOI: 10.5281/zenodo.16995424
title: Experimental data, processing and simulation scripts for CHEESY ENDOR

description: Data, processing and simulation scripts for the manuscript: "Resolving spectral overlap in ENDOR by chirp echo Fourier transform detection"All raw data (as .mat files) and MATLAB processing scripts for Figures of the manuscript + SI are supplied. 

For both ScoI and BDPA additional data on chirp echo optimization, excitation transfer function measurements (resonator profiles) and ENDOR nutations is added.

Most processing functions need helper functions to work. These can be found in the folder 'helpers', which is best added to the MATLAB path.

Simulation scripts are found in the 'simulations' folder. The cheesy endor simulation is called 'wasabi' and is called in all other files of the folder to obtain the simulated cheesy endor spectrum.Simulations are based on the EasySpin package, which needs to be in the MATLAB path for the simulations to work.
DOI: 10.6075/j0cj8ccw
title: CIL:40506, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Quick-freeze deep-etch image of rows of carrier vesicles lined up along the cytopharyngeal microtubular ribbons. These vesicles arise from early endosomes as clathrin coated vesicles and are about 100nm in diameter. Vesicles lose their coats before binding with the dynein motors that link them to the microtubules. They tend to lie on the anterior side of the ribbons along with the discoidal vesicles. Carrier vesicles eventually dock on acidosomes and fuse with these. Acidosomes are late endosomes. TEM taken on 5/24/88 by C. Schroeder with Zeiss 10A operating at 80kV. Neg. 12,000X. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/). Small part published in J. Cell Biol. 111:2553-2562, 1990. Adapted with permission.
description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0kw5dxn
title: CIL:40500, Homo sapiens, epidermoid carcinoma. In Cell Image Library

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.
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; 4',6-diamidino-2-phenylindole (DAPI)
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 
 HPA044440 (shown in green). HPA044440 is a polyclonal Anti-NOL8 antibody that stains the nucleus and the nucleoli. 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 and (red).