cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0765dgt
title: CIL:10498, Toxoplasma gondii RH. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image; charge coupled device (CCD)
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP; mCherryFP
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: A monolayer of human foreskin fibroblast cells was infected with Toxoplasma gondii expressing EGFP-tagged TgCentrin2 and mCherry-tagged TgIMC1 (innermembrane complex scaffold protein). Images acquired using API DeltaVision on a Olympus IX70 inverted microscope. Objective: Olympus 100X oil immersion, 1.35 NA. Filters: EGFP, ex 450-490 em 500-540, mCherry, ex 555-592 em 600-665. Dichromatic mirror: Chroma 89021. Captured with CoolSnapHQ/ICX285. Unpublished image that is similar to images published in PMID: 16518471. See publication for other experimental details.
DOI: 10.15468/dl.cqb3pv
title: Occurrence Download

description: A dataset containing 1582 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "TaxonKey is Passer montanus",
 "Year 2025-2025"
 ]
}

 The dataset includes 1582 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009516-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17168323
title: Early-life high-dose sodium butyrate supplementation inhibits growth via sterol metabolism in 15-month-old dairy cattle: insights from gastrointestinal microbiota and host metabolism

description: Sodium butyrate is a common calf feed additive, but its long-term effects are unknown. This study found that feeding high doses in milk before weaning had a negative programming effect, stunting growth in heifers at 15 months of age. This was caused by disrupting rumen microbes and cholesterol metabolism. Our results provide dairy farmers and nutritionists with crucial guidance: optimizing butyrate dosage is essential to avoid unintended losses in growth and productivity, ensuring sustainable and economical dairy production.
DOI: 10.24435/materialscloud:2v-n2
title: Magnons in chromium trihalides calculated with the ab initio Bethe-Salpeter equation

description: In this paper, we present and benchmark our first-principles calculations of magnon dispersions and wave functions in monolayer Cr trihalides using the finite-momentum Bethe-Salpeter equation (BSE) to describe collective spin-flip excitations. We study the dependence of magnon dispersions on the halide species and resolve the small topological gap at the Dirac point in the magnon spectrum by including spin-orbit coupling. We analyze the obtained magnon wave functions to gain insight into magnon states in real and reciprocal space. We also compare our method with the Heisenberg spin model. This work advances the quantitative modeling of magnons, providing the starting point for studying magnon interactions in a first-principles BSE framework.

This archive includes all the inputs for DFT calculations in QuantumEspresso and GW-BSE with the Yambo code to reproduce the data in our paper.
DOI: 10.24435/materialscloud:vd-fv
title: Magnons in chromium trihalides calculated with the ab initio Bethe-Salpeter equation

description: In this paper, we present and benchmark our first-principles calculations of magnon dispersions and wave functions in monolayer Cr trihalides using the finite-momentum Bethe-Salpeter equation (BSE) to describe collective spin-flip excitations. We study the dependence of magnon dispersions on the halide species and resolve the small topological gap at the Dirac point in the magnon spectrum by including spin-orbit coupling. We analyze the obtained magnon wave functions to gain insight into magnon states in real and reciprocal space. We also compare our method with the Heisenberg spin model. This work advances the quantitative modeling of magnons, providing the starting point for studying magnon interactions in a first-principles BSE framework.

This archive includes all the inputs for DFT calculations in QuantumEspresso and GW-BSE with the Yambo code to reproduce the data in our paper.
DOI: 10.15468/dl.ujag6y
title: Occurrence Download

description: A dataset containing 22143 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Potamogeton trichoides"
 ]
}

 The dataset includes 22143 records from 434 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009519-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17491662
title: Total rRNAs gene  copies and their location within the genome of Yellowfin tuna (Thunnus albacares) as obtained from GenBank.

description: These are the total copies of ribosomal RNAs (5S, 5.8S, 18S, and 28S rRNA) and their chromosomal locations in the Yellowfin tuna (Thunnus albacares) genome. And this dada as a supplementary part of this following Manuscript:

Molecular approach to unbiased staging of ovarian development in tuna (Thunnus albacares) fish 

Joyanta Bir*1,3, Oihane Diaz de Cerio1, Maren Ortiz-Zarragoitia1, Patricia Lastra Luque2, Deniz Kukul2, Iker Zudaire2, and Ibon Cancio1

1CBET Research Group, Dept. of Zoology & Animal Cell Biology, Centre for Experimental Marine Biology & Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Areatza 47, 48620, Plentzia, Spain

2AZTI Marine Research, Basque Research and Technology Alliance (BRTA), Herrera Kaia Portualdea z/g, 20110 Pasaia, Spain 

3Fisheries and Marine Resources Technology Discipline, School of Life Sciences, Khulna University, Khulna, 9208, Bangladesh
DOI: 10.5281/zenodo.17491663
title: Total rRNAs gene  copies and their location within the genome of Yellowfin tuna (Thunnus albacares) as obtained from GenBank.

description: These are the total copies of ribosomal RNAs (5S, 5.8S, 18S, and 28S rRNA) and their chromosomal locations in the Yellowfin tuna (Thunnus albacares) genome. And this dada as a supplementary part of this following Manuscript:

Molecular approach to unbiased staging of ovarian development in tuna (Thunnus albacares) fish 

Joyanta Bir*1,3, Oihane Diaz de Cerio1, Maren Ortiz-Zarragoitia1, Patricia Lastra Luque2, Deniz Kukul2, Iker Zudaire2, and Ibon Cancio1

1CBET Research Group, Dept. of Zoology & Animal Cell Biology, Centre for Experimental Marine Biology & Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Areatza 47, 48620, Plentzia, Spain

2AZTI Marine Research, Basque Research and Technology Alliance (BRTA), Herrera Kaia Portualdea z/g, 20110 Pasaia, Spain 

3Fisheries and Marine Resources Technology Discipline, School of Life Sciences, Khulna University, Khulna, 9208, Bangladesh
DOI: 10.6075/j0d50mjh
title: CIL: 52765, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given tile position
description: Tile x=7, y=2, z=5 from PS11_10021_2B_Myc_Terc
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
DOI: 10.6075/j0qv3kn8
title: CIL:10012, Didinium nasutum, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: The locomotor cortex of Didinium. A longitudinal section of basal bodies and the axonemes of cilia is revealed as they emerge from the cell cortex of Didinium. Bundles of microtubules extend from the basal bodies into the endoplasm through the fibrous layer that characterizes the cortex of Didinium. Tubular or flattened early endosomes with coated pits at their margins are present in the endoplasm beneath the fibrous layer. Mitochondrial cristae appear to be decorated by F1F0 ATP synthases. Cross sections of three bacteria are noted between the cilia. TEM taken on 5/9/69 by M. Sage with Philips 300 operating at 60kV. Neg. 14,800X. Bar = 0.5µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. A raw, unprocessed, high resolution version of this image (CIL:4661) is in the library and available 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: film; Print from negative scanned for Photoshop.
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j0c53jt3
title: CIL:36021, damselfly, flight muscle cell. In Cell Image Library

description: Negatives scanned at LBL then reduced in size for upload TEM magnifications not currently available. Scan step size is 6.3 micron, then reduced in size 4X for upload, for an effective pixel size of 25 micron. 

Heads and tail were removed, the thorax was bisected and immersed in 100 mM KCl, 10 mM EDTA, 10 Triton X for a few hrs, to depolarize and skin the fibers, then maintained at -20 C in 50% glycerol in the same solution for several weeks to induce rigor by eliminating ATP. The muscle was gently homogenized in a waring blender in 0.9% NaCl. The fibrils were deposited on glass and sequentially fixed in 0.1% glutaraldehyde in 0.1 M cacodylate buffer, rinsed in 100 mM ammonium acetate, treated with 1% uranyl acetate for 30 seconds, rinsed in 40% methanol and frozen in liquid nitrogen. The fibrils were freeze dried at -90 C for 30 minutes and rotary shadowed with platinum either at 25C or 45C in a Balzer's 400 freeze fracture. The glass was dissolved in hydrofluoric acid and the replicas were mounted on copper grids and examined in a Philips 410 Microscope.
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;spatialmeasurements
description: The image shows the surface of the ribbon-like myofibrils, with some remnants of the SR attached mostly at the Z lines. The regular disposition of attached cross bridges is visible in many areas. Most images of this group 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. 
 
References for the image: 
Loesser, K.E. and Franzini-Armstrong, C. A simple method for freeze-drying of macromolecules and macromolecular complexes. J. Struct. Biol. 103: 48-56, 1990. Bard, F., Franzini-Armstrong, C. and Ip W. Rigor cross bridges are double headed in fast muscle from crayfish. J. Cell Biol. 105: 2225-2234, 1987.
DOI: 10.6075/j0pn94gj
title: CIL:24813, Saccharomyces cerevisiae S288c. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: mCherryFP
Processing history: constrained iterative deconvolution
Data qualification: Processed;spatialmeasurements;intensitiesquantitation
description: Sec63-mCherry in BY4742 sac1∆ vps74∆ highlights nuclear ER and cortical ER and/or PM. This image is the control image labeling ER for overlay with GFP-Vps74 (CIL# 24812) demonstrating that in the sac1∆ vps74∆ mutant, GFP-Vps74 localizes, in addition to the Golgi apparatus, to nuclear ER and cortical ER and/or PM. SAC1 encodes an integral membrane phosphoinositide phosphatase that is localized to the ER and Golgi. Cells grown in liquid medium were mounted in growth medium and 3D image stacks were collected at 0.4-µm z increments on a DeltaVision workstation (Applied Precision) based on an inverted microscope (IX-70; Olympus) using a 100× NA 1.4 oil immersion lens. Images were captured at 23C with a 12-bit CCD camera (CoolSnap HQ; Photometrics) and deconvolved using the iterative-constrained algorithm (Agard, 1984) and the measured point spread function. One image from the approximate center of z stack is shown in Fig1B Sec63 (ER)/sac1∆ panel (overlay CIL#24812/24813 in merge panel) in J Cell Biol. 187: 967-975. 2009. Images in Fig 1B include CIL#s 24815, 24812, 24813.
DOI: 10.6075/j00p0zcv
title: CIL: 50699, FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles: 3.3_Cell_3_Stack_Filtered. In Cell Image Library

description: Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample. 
3.3_Cell_3_Stack_Filtered is a multipage TIFF file (2.6×2.6×15 nm³ voxel size) filtered with mean shift filter (kernel: 3D, 3 &gt; max distance X & Y: 3 &gt; noise spread: 1.0), unsharp filter (unit: 8 &gt; kernel: 3D, 3 &gt; standard deviation: 1.0 &gt; unsharp factor: 1.0) and histogram balancing filter (set to reference image #170).
This file is a part of Dataset 3, comprised of files related to the Cell #3 of current study. The numbering order of the files reflects the order of operations performed during the analysis.
description: Imaging mode: Serial Electron Microscopy; Focused Ion Beam Scanning Electron Microscopy (FIB-SEM)
Visualization methods: Heavy metal stain (Osmium Tetroxide, Potassium Ferrocyanide, Tannic Acid); Immunogold labeling with 10 nm gold beads
description: FIB-SEM Dataset of anti-PKHD1L1 Immuno-Gold Labeled Outer Hair Cell Stereocilia Bundles. Postnatal day 4 mouse Inner Ear Organ of Corti labeled with anti-PKHD1L1 antibody (10 nm gold beads). The dataset represents the apical end of the Outer Hair Cell with the stereocilium bundle. Images were acquired with FEI Helios FIB-SEM, using backscatter detector from an epoxy resin embedded inner ear Organ of Corti sample.
DOI: 10.6075/j0ft8k0t
title: CIL:36102, damselfly, flight muscle cell. In Cell Image Library

description: The image shows the surface of the ribbon-like myofibrils, with some remnants of the SR attached mostly at the Z lines. The regular disposition of attached cross bridges is visible in many areas. Most images of this group 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. 
 
References for the image: 
Loesser, K.E. and Franzini-Armstrong, C. A simple method for freeze-drying of macromolecules and macromolecular complexes. J. Struct. Biol. 103: 48-56, 1990. Bard, F., Franzini-Armstrong, C. and Ip W. Rigor cross bridges are double headed in fast muscle from crayfish. J. Cell Biol. 105: 2225-2234, 1987.
description: Negatives scanned at LBL then reduced in size for upload TEM magnifications not currently available. Scan step size is 6.3 micron, then reduced in size 4X for upload, for an effective pixel size of 25 micron. 

Heads and tail were removed, the thorax was bisected and immersed in 100 mM KCl, 10 mM EDTA, 10 Triton X for a few hrs, to depolarize and skin the fibers, then maintained at -20 C in 50% glycerol in the same solution for several weeks to induce rigor by eliminating ATP. The muscle was gently homogenized in a waring blender in 0.9% NaCl. The fibrils were deposited on glass and sequentially fixed in 0.1% glutaraldehyde in 0.1 M cacodylate buffer, rinsed in 100 mM ammonium acetate, treated with 1% uranyl acetate for 30 seconds, rinsed in 40% methanol and frozen in liquid nitrogen. The fibrils were freeze dried at -90 C for 30 minutes and rotary shadowed with platinum either at 25C or 45C in a Balzer's 400 freeze fracture. The glass was dissolved in hydrofluoric acid and the replicas were mounted on copper grids and examined in a Philips 410 Microscope.
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;spatialmeasurements
DOI: 10.6075/j05b01q8
title: CIL:1660, 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 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/j0ft8kg3
title: CIL: 51802, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

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
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/j0jw8dmf
title: CIL: 54000. In Cell Image Library

description: Visualization methods: confocal microscopy
description: STE family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
DOI: 10.6075/j00k276n
title: CIL:37207, Rattus, cardiac muscle cell. In Cell Image Library

description: Transmission electron micrograph of longitudinal section of rat heart cardiac muscle from the atrium. A darkly stained intercalated disc runs from upper left to lower right. Also prominent are groups of myofibrils running diagonally across the image and several mitochondria. 
 This 1960 TEM image has historical value as one of the earliest views of muscle ultrastructure.
 Image made available by James D. Jamieson and the Department of Cell Biology, Yale University School of Medicine.
description: Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi. Original Magnification: x20,000.
description: Preparation: chemically fixed tissue
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