cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0c24w8d
title: CIL:36869, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EYFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Specifications of the custom built two-photon microscope, including the laser sources, signal amplification, PMT specifications, and YFP filter sets are described in: 
Ruthazer ES, Li J, Cline HT. 2006. Stabilization of axon branch dynamics by synaptic maturation. J Neurosci 26(13):3594-3603. 

The methods of cell transfection with electroporation can be found here: 
Bestman JE, Ewald RC, Chiu S-L, Cline HT. 2006. In vivo single-cell electroporation for transfer of DNA and macromolecules. Nat Protocols 1(3):1267-1272. 

Further explanation can be found here:
Bestman JE, Cline HT. 2008. The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo. Proc Natl Acad Sci U S A 105(51):20494-20499.

Bestman JE, Cline HT. 2009. The Relationship between Dendritic Branch Dynamics and CPEB-Labeled RNP Granules Captured in Vivo. Front Neural Circuits 3:10.
description: This is IMAGE #2 (10 minutes) of a time lapse series contained with in this image group. It shows neurons from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47.
 
 The images were acquired with ~10 minute intervals and show morphological plasticity of the dendritic arbor with branch additions and retractions.
 
 These cells were transfected ~24 hours earlier with in vivo electroporation of plasmid DNA encoding eYFP. The intact, living tadpole was anesthetized, positioned under a glass coverslip and this image was taken directly through its transparent skin using a custom built two-photon microscope.
 
 Images were acquired a 0, 10, 20, 30, and 50 minutes. After 60 minutes, the animal was placed in a 50 microMolar anisomycin solution for ~4 hours. A second time lapse series (10 minute interval for 60 minutes) was then acquired.
DOI: 10.6075/j09g5mpc
title: CIL:37058, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Specifications of the custom built two-photon microscope, including the laser sources, signal amplification, PMT specifications, and YFP filter sets are described in: 
Ruthazer ES, Li J, Cline HT. 2006. Stabilization of axon branch dynamics by synaptic maturation. J Neurosci 26(13):3594-3603. 

The methods of cell transfection with electroporation can be found here: 
Bestman JE, Ewald RC, Chiu S-L, Cline HT. 2006. In vivo single-cell electroporation for transfer of DNA and macromolecules. Nat Protocols 1(3):1267-1272. 

Further explanation can be found here:
Bestman JE, Cline HT. 2008. The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo. Proc Natl Acad Sci U S A 105(51):20494-20499.

Bestman JE, Cline HT. 2009. The Relationship between Dendritic Branch Dynamics and CPEB-Labeled RNP Granules Captured in Vivo. Front Neural Circuits 3:10.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: This is IMAGE #6 (hour 8) of a developing neuron from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47. 
 The cell was imaged at a 2 hour intervals over 8 hours and shows the development and morphological plasticity of the dendritic arbor and axon over time.This image is part of an image group.
 
 
 The cell was transfected with in vivo electroporation of plasmid DNA encoding eGFP ~24 hours before the image was acquired. The intact, living tadpole was anesthetized, positioned under a glass coverslip and this image was taken directly through its transparent skin using a custom built two-photon microscope.
DOI: 10.6075/j0wh2ptg
title: CIL:36997, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EYFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Specifications of the custom built two-photon microscope, including the laser sources, signal amplification, PMT specifications, and YFP filter sets are described in: 
Ruthazer ES, Li J, Cline HT. 2006. Stabilization of axon branch dynamics by synaptic maturation. J Neurosci 26(13):3594-3603. 

The methods of cell transfection with electroporation can be found here: 
Bestman JE, Ewald RC, Chiu S-L, Cline HT. 2006. In vivo single-cell electroporation for transfer of DNA and macromolecules. Nat Protocols 1(3):1267-1272. 

Further explanation can be found here:
Bestman JE, Cline HT. 2008. The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo. Proc Natl Acad Sci U S A 105(51):20494-20499.

Bestman JE, Cline HT. 2009. The Relationship between Dendritic Branch Dynamics and CPEB-Labeled RNP Granules Captured in Vivo. Front Neural Circuits 3:10.
description: This is IMAGE #1 (day 1) of a time lapse series contained with in this image group. It shows two neurons from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47. Autofluorescent pigment cells are visible in the superficial layers of the z-stack. 
 
 The images were acquired daily over 2 days and show dendritic arbor development and morphological plasticity of the dendritic arbor with branch additions and retractions.
 
 The cell was transfected with in vivo electroporation of plasmid DNA encoding eYFP ~24 hours before the first image was acquired. The intact, living tadpole was anesthetized, positioned under a glass coverslip and this image was taken directly through its transparent skin using a custom built two-photon microscope.
DOI: 10.15468/dl.6jtq5w
title: Occurrence Download

description: A dataset containing 1395 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Birds - Wild Birds (KIDR-BI)"
 ]
}

 The dataset includes 1395 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009734-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hm6bp8
title: Occurrence Download

description: A dataset containing 1054 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Royal Botanic Gardens, Kew - Herbarium Specimens",
 "TaxonKey is one of (Isoberlinia, Afzelia)"
 ]
}

 The dataset includes 1054 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009733-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17493424
title: Re-analysis Package: LLM Summarization for Log Analysis

description: This is a package containing scripts and data collected for a research paper about using LLM Summarization to support fault localization during log analysis.

The data includes: 1) CSV files and analysis scripts for cognitive load measures using the NASA TLX measures, 2) Interview guide and labeled quotes from a thematic analysis with practitioners.

Details are shared in the paper (under submission), and in the README.md file in this package.
DOI: 10.5281/zenodo.17493425
title: Re-analysis Package: LLM Summarization for Log Analysis

description: This is a package containing scripts and data collected for a research paper about using LLM Summarization to support fault localization during log analysis.

The data includes: 1) CSV files and analysis scripts for cognitive load measures using the NASA TLX measures, 2) Interview guide and labeled quotes from a thematic analysis with practitioners.

Details are shared in the paper (under submission), and in the README.md file in this package.
DOI: 10.6075/j0q81bt0
title: CIL:50637, Homo sapiens, monocyte. In Cell Image Library

description: Imaging mode: microscopy
Visualization methods: x100
description: One monocyte contained an erythrocyte. Two other erythrocytes are at contact to other monocytes, these cells appear ar partly lytic.
description: Cerebrospinal fluid, cytocentrifugation, May-Grunwald-Giemsa stain.
DOI: 10.6075/j07p8x15
title: CIL:50659, Homo sapiens, Umbilical vein endothelial cell. In Cell Image Library

description: Human umbilical vein endothelial cells stained initially for nuclei with DAPI (blue) and for vascular endothelial cadherin (red)
description: Image was acquired with 40x lens of Olympus BX60 fluorescence microscope. ImageJ merge channels function was used to generate the image. Nuclei-stained blue regions replaced with cyan for clarity.
description: Preparation: Cells plated on a 0.2% gelatin-coated chamber slide
Item type: recorded image
Imaging mode: fluorescence 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)
DOI: 10.6075/j0vq31s9
title: CIL:8779, Rattus, multipolar neuron. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
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 epitope; differences in adsorption or binding of stain
Visualization methods: phalloidin; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
description: This color combined image shows the spatial relationship between filamentous actin (red) and microtubule array (green) in cultured hippocampal neurons, grown for 1 day in vitro. Actin staining (with rhodamine phalloidin) highlights the growing tips and filopodial extensions along axons and dendrites, while microtubule staining reveals the stable shafts of these processes.
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, 37°C, 15 minutes), permeabilized (0.25% Triton, 7 minutes) and immunostained for tubulin (monoclonal DM1A, Sigma, with Alexa 488 conjugated secondary, Molecular Probes, excitation, 494, emission, 519) and rhodamine-conjugated phalloidin (Molecular Probes, excitation, 540, emission, 565). Images were acquired with a Leica DMRA microscope with a mercury arc lamp, a 40X lens (HCX PL Fluotar, NA 0.75), Leica GFP filter set (excitation, BP 470/40; dichromatic mirror, 500, suppression filter, BP 525/50); Leica N3 filter set (excitation, BP546/12; dichromatic mirror, 565, suppression filter, BP 600/40), Photometrics CoolSnap ES CCD camera and MetaMorph software. Merged image was generated with the MetaMorph color combine function.
DOI: 10.6075/j09p30f3
title: CIL:50663, rat, cortical primary neurons. In Cell Image Library

description: Item type: recorded image
Imaging mode: Multi-tilt electron tomography
description: Tomogram, 2 tilts. A protein-fragment complementation assay (PCA) for detecting and localizing intracellular protein-protein interactions (PPIs) was built by bisection of miniSOG, a fluorescent flavoprotein derived from the light, oxygen, voltage (LOV)-2 domain of Arabidopsis phototropin. When brought together by interacting proteins, the fragments reconstitute a functional reporter that permits tagged protein complexes to be visualized by fluorescence light microscopy (LM), and then by standard as well as “multicolor” electron microscopy (EM) via the photooxidation of 3-3′-diaminobenzidine and its derivatives.
description: Alpha-synuclein aggregates in the cell body of primary neurons expressing the reconstituted miniSOG-Jα.
DOI: 10.60893/figshare.jcp.30168475
title: Supplementary Material for "Machine learning workflow for analysis of high-dimensional order parameter space: A case study of polymer crystallization from molecular dynamics simulations"

description: Figures, additional results, and details referenced in the main text.
This was the pre-revision version.
DOI: 10.6075/j0qn65cs
title: CIL:50661, Homo sapiens, Umbilical vein endothelial cell. In Cell Image Library

description: Image was acquired with 60x lens of Olympus BX60 fluorescence microscope. ImageJ merge channels function was used to generate the image. Nuclei-stained blue regions replaced with cyan for clarity.
description: Human umbilical vein endothelial cells stained initially for nuclei with DAPI (blue) and for vascular endothelial cadherin (red).
description: Preparation: Cells plated on a 0.2% gelatin-coated chamber slide
Item type: recorded image
Imaging mode: fluorescence 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)
DOI: 10.60893/figshare.jcp.30168475.v1
title: Supplementary Material for "Machine learning workflow for analysis of high-dimensional order parameter space: A case study of polymer crystallization from molecular dynamics simulations"

description: Figures, additional results, and details referenced in the main text.
This was the pre-revision version.
DOI: 10.6075/j02z1450
title: CIL:50660, Homo sapiens, Umbilical vein endothelial cell. In Cell Image Library

description: Preparation: Cells plated on a 0.2% gelatin-coated chamber slide
Item type: recorded image
Imaging mode: fluorescence 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)
description: Image was acquired with 40x lens of Olympus BX60 fluorescence microscope. ImageJ merge channels function was used to generate the image. Nuclei-stained blue regions replaced with cyan for clarity.
description: Human umbilical vein endothelial cells stained initially for nuclei with DAPI (blue) and for vascular endothelial cadherin (red).
DOI: 10.6075/j01z431m
title: CIL:50649, Homo sapiens, Umbilical vein endothelial cell. In Cell Image Library

description: Preparation: Cells plated on a 0.2% gelatin-coated chamber slide
Item type: recorded image
Imaging mode: fluorescence 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)
description: Human umbilical vein endothelial cells stained initially for nuclei with DAPI (blue) and for vascular endothelial cadherin (red).
description: Image was acquired with a 40x lens of an Olympus BX60 fluorescence microscope. ImageJ merge channels function was used to generate the image. Nuclei-stained blue regions replaced with cyan for clarity.
DOI: 10.6075/j0j38r5t
title: CIL:50647, Homo sapiens, Umbilical vein endothelial cell. In Cell Image Library

description: Human umbilical vein endothelial cells stained initially for nuclei with DAPI (blue) and for vascular endothelial cadherin (red).
description: Preparation: Cells plated on a 0.2% gelatin-coated chamber slide
Item type: recorded image
Imaging mode: fluorescence 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)
description: Image was acquired with a 40x lens of an Olympus BX60 fluorescence microscope. ImageJ merge channels function was used to generate the image. Nuclei-stained blue regions replaced with red and vascular endothelial cadherin-stained red regions replaced with cyan for clarity
DOI: 10.6075/j08914qg
title: CIL:50639, Mus musculus. In Cell Image Library

description: Zeiss Xradia 510 Versa (Zeiss X-Ray Microscopy) operated at 40 kV (76 µA current) with ×40 magnification . Tilt series of 3201 projections using XMReconstructor (Xradia). Mouse brain, hippocampal section, from the center of the suprapyramidal blade of the dentate gyrus (DG) to the molecular layer
description: As biological imaging datasets increase in size, deep neural networks are considered vital tools for efficient image segmentation. While a number of different network architectures have been developed for segmenting even the most challenging biological images, community access is still limited by the difficulty of setting up complex computational environments and processing pipelines, and the availability of compute resources. Here, we address these bottlenecks, providing a ready-to-use image segmentation solution for any lab, with a pre-configured, publicly available, cloud-based deep convolutional neural network on Amazon Web Services (AWS). We provide simple instructions for training and applying CDeep3M for segmentation of large and complex 2D and 3D microscopy datasets of diverse biomedical imaging modalities.
description: Item type: X-ray micrograph
Imaging mode: recorded image
DOI: 10.6075/j0jw8chp
title: CIL:50658, Homo sapiens, Umbilical vein endothelial cell. In Cell Image Library

description: Image was acquired with 60x lens of Olympus BX60 fluorescence microscope. ImageJ merge channels function was used to generate the image. Nuclei-stained blue regions replaced with cyan for clarity.
description: Preparation: Cells plated on a 0.2% gelatin-coated chamber slide
Item type: recorded image
Imaging mode: fluorescence microscopy
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody; 4',6-diamidino-2-phenylindole (DAPI)
description: Human umbilical vein endothelial cells stained initially for nuclei with DAPI (blue) and for vascular endothelial cadherin (red).
DOI: 10.6075/j0td9vzb
title: CIL:50656, Homo sapiens, Umbilical vein endothelial cell. In Cell Image Library

description: Image was acquired with 60x lens of Olympus BX60 fluorescence microscope. ImageJ merge channels function was used to generate the image. Nuclei-stained blue regions replaced with red and vascular endothelial cadherin-stained red regions replaced with cyan for clarity.
description: Human umbilical vein endothelial cells stained initially for nuclei with DAPI (blue) and for vascular endothelial cadherin (red).
description: Preparation: Cells plated on a 0.2% gelatin-coated chamber slide
Item type: recorded image
Imaging mode: fluorescence 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)
DOI: 10.6075/j0h41q10
title: CIL:50653, Homo sapiens, Umbilical vein endothelial cell. In Cell Image Library

description: Preparation: Cells plated on a 0.2% gelatin-coated chamber slide
Item type: recorded image
Imaging mode: fluorescence 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)
description: Human umbilical vein endothelial cells stained initially for nuclei with DAPI (blue) and for vascular endothelial cadherin (red)
description: Image was acquired with 60x lens of Olympus BX60 fluorescence microscope. ImageJ merge channels function was used to generate the image. Nuclei-stained blue regions replaced with cyan for clarity.
DOI: 10.6075/j0cc0z98
title: CIL:50652, Homo sapiens, Umbilical vein endothelial cell. In Cell Image Library

description: Human umbilical vein endothelial cells stained initially for nuclei with DAPI (blue) and for vascular endothelial cadherin (red).
description: Preparation: Cells plated on a 0.2% gelatin-coated chamber slide
Item type: recorded image
Imaging mode: fluorescence 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)
description: Image was acquired with 60x lens of Olympus BX60 fluorescence microscope. ImageJ merge channels function was used to generate the image. Nuclei-stained blue regions replaced with cyan for clarity.
DOI: 10.6075/j01c1x1j
title: CIL:50676, Drosophila melanogaster. In Cell Image Library

description: We show in this study that brain and intestinal stem cells of Drosophila contain a new type of cytoplasmic protrusion which is enriched in mitochondria and that the mitochondria are probably dependent on microtubules for their distribution. The protrusions form mitochondria-enriched cytoplasmic bridges from the stem cells to their niche that we speculate are important in regulating stem cell quiescence and activation.
description: Specimen preparation: Larval brains (LBs) were prepared from starved (amino acid-restricted) first instar (L1) larvae to enrich for quiescent neural stem cells. The LBs were glutaraldehyde-fixed, tannic acid and OsO4-stained, embedded in resin, thin-sectioned (60-70 nm) and stained with uranyl acetate/lead citrate, then observed by TEM.
description: Item type: Digital
Imaging mode: CM12 TEM equipped with AMT digital camera
DOI: 10.6075/j0rx9c7p
title: CIL:50675, Drosophila melanogaster. In Cell Image Library

description: Specimen preparation: Larval brains (LBs) were prepared from starved (amino acid-restricted) first instar (L1) larvae to enrich for quiescent neural stem cells. The LBs were glutaraldehyde-fixed, tannic acid and OsO4-stained, embedded in resin, thin-sectioned (60-70 nm) and stained with uranyl acetate/lead citrate, then observed by TEM.
description: We show in this study that brain and intestinal stem cells of Drosophila contain a new type of cytoplasmic protrusion which is enriched in mitochondria and that the mitochondria are probably dependent on microtubules for their distribution. The protrusions form mitochondria-enriched cytoplasmic bridges from the stem cells to their niche that we speculate are important in regulating stem cell quiescence and activation.
description: Item type: Digital
Imaging mode: CM12 TEM equipped with AMT digital camera
DOI: 10.6075/j0542nrv
title: CIL:50673, Drosophila melanogaster. In Cell Image Library

description: Item type: Digital
Imaging mode: CM12 TEM equipped with AMT digital camera
description: Specimen preparation: Larval brains (LBs) were prepared from starved (amino acid-restricted) first instar (L1) larvae to enrich for quiescent neural stem cells. The LBs were glutaraldehyde-fixed, tannic acid and OsO4-stained, embedded in resin, thin-sectioned (60-70 nm) and stained with uranyl acetate/lead citrate, then observed by TEM.
description: We show in this study that brain and intestinal stem cells of Drosophila contain a new type of cytoplasmic protrusion which is enriched in mitochondria and that the mitochondria are probably dependent on microtubules for their distribution. The protrusions form mitochondria-enriched cytoplasmic bridges from the stem cells to their niche that we speculate are important in regulating stem cell quiescence and activation.