1,721,004 research outputs found
Automatic nuclei segmentations in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse epididymis (jrc_mus-epididymis-1) model
No full textModel description: Cellpose 2.0 was trained on nuclei from 24 2D slices from jrc_mus-epididymis-1.Architecture: Cellpose 2.0Input voxel size (nm): 128 x 128 x 128 (x, y, z)Output voxel size (nm): 128 x 128 x 128 (x, y, z)Classes trained on: NucleusGPU: RTX A6000RAM: 256.0 GiBSoftware: Cellpose 2.0Software DOI: https://doi.org/10.1038/s41592-022-01663-4Source dataset (EM) ID: jrc_mus-epididymis-1Source dataset (EM) DOI: https://doi.org/10.25378/janelia.22190377Generated dataset DOI: https://doi.org/10.25378/janelia.25355719Model URL (redirect): https://data.janelia.org/uXpZXGithub repo: https://github.com/janelia-cellmap/cellmap-modelsVisualization website: https://openorganelle.janelia.org/datasets/jrc_mus-epididymis-1</p
Automatic nuclei segmentations in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of P7 mouse heart (jrc_mus-heart-1) model
No full textModel description: Cellpose 2.0 was trained on nuclei from 25 2D slices from jrc_mus-heart-1.Architecture: Cellpose 2.0Input voxel size (nm): 128 x 128 x 128 (X, Y, Z)Output voxel size (nm): 128 x 128 x 128 (X, Y, Z)Classes trained on: NucleusGPU: RTX A6000RAM: 256.0 GiBWall time (sec): 2334.71Software: Cellpose 2.0Software DOI: https://doi.org/10.1038/s41592-022-01663-4Source dataset (EM) ID: jrc_mus-heart-1Source dataset (EM) DOI: https://doi.org/10.25378/janelia.24020919Generated dataset DOI: https://doi.org/10.25378/janelia.25352203Model URL (redirect): https://data.janelia.org/8p9VpGithub repo: https://github.com/janelia-cellmap/cellmap-modelsVisualization website: https://openorganelle.janelia.org/datasets/jrc_mus-heart-1</p
Automatic nuclei segmentations in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse epididymis (jrc_mus-epididymis-2) model
No full textModel description: Cellpose 2.0 was trained on nuclei from 21 2D slices from jrc_mus-epididymis-2.Architecture: Cellpose 2.0Input voxel size (nm): 128 x 128 x 128 (x, y, z)Output voxel size (nm): 128 x 128 x 128 (x, y, z)Classes trained on: NucleusGPU: RTX A6000RAM: 256.0 GiBSoftware: Cellpose 2.0Software DOI: https://doi.org/10.1038/s41592-022-01663-4Source dataset (EM) ID: jrc_mus-epididymis-2Source dataset (EM) DOI: https://doi.org/10.25378/janelia.23407907Generated dataset DOI: https://doi.org/10.25378/janelia.25355689Model URL (redirect): https://data.janelia.org/cDhv3Github repo: https://github.com/janelia-cellmap/cellmap-modelsVisualization website: https://openorganelle.janelia.org/datasets/jrc_mus-epididymis-2</p
Automatic nuclei segmentations in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of P7 mouse liver (jrc_mus-liver-3) model
No full textModel description: Cellpose 2.0 was trained on nuclei from 17 2D slices from jrc_mus-liver-3.Architecture: Cellpose 2.0Input voxel size (nm): 128 x 128 x 128 (X, Y, Z)Output voxel size (nm): 128 x 128 x 128 (X, Y, Z)Classes trained on: NucleusGPU: NVIDIA TITAN RTXRAM: 768.0 GiBWall time (sec): 1552.44Software: Cellpose 2.0Software DOI: https://doi.org/10.1038/s41592-022-01663-4Source dataset (EM) ID: jrc_mus-liver-3Source dataset (EM) DOI: https://doi.org/10.25378/janelia.24051189Generated dataset DOI: https://doi.org/10.25378/janelia.25352218Model URL (redirect): https://data.janelia.org/frnMsGithub repo: https://github.com/janelia-cellmap/cellmap-modelsVisualization website: https://openorganelle.janelia.org/datasets/jrc_mus-liver-3</p
Automatic nuclei segmentations in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of P7 mouse skin (jrc_mus-skin-1) model
No full textModel description: Cellpose 2.0 was trained on nuclei from 11 2D slices from jrc_mus-skin-1.Architecture: Cellpose 2.0Input voxel size (nm): 128 x 128 x 128 (X, Y, Z)Output voxel size (nm): 128 x 128 x 128 (X, Y, Z)Classes trained on: NucleusGPU: RTX A6000RAM: 256.0 GiBSoftware: Cellpose 2.0Software DOI: https://doi.org/10.1038/s41592-022-01663-4Source dataset (EM) ID: jrc_mus-skin-1Source dataset (EM) DOI: https://doi.org/10.25378/janelia.24085269Generated dataset DOI: https://doi.org/10.25378/janelia.25352227Model URL (redirect): https://data.janelia.org/R2Av1Github repo: https://github.com/janelia-cellmap/cellmap-modelsVisualization website: https://openorganelle.janelia.org/datasets/jrc_mus-skin-1</p
Automatic nuclei segmentations in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of P7 mouse thymus (jrc_mus-thymus-1) model
No full textModel description: Cellpose 2.0 was trained on nuclei from 20 2D slices from jrc_mus-thymus-1.Architecture: Cellpose 2.0Input voxel size (nm): 128 x 128 x 128 (X, Y, Z)Output voxel size (nm): 128 x 128 x 128 (X, Y, Z)Classes trained on: NucleusGPU: RTX A6000RAM: 256.0 GiBSoftware: Cellpose 2.0Software DOI: https://doi.org/10.1038/s41592-022-01663-4Source dataset (EM) ID: jrc_mus-thymus-1Source dataset (EM) DOI: https://doi.org/10.25378/janelia.24085287Generated dataset DOI: https://doi.org/10.25378/janelia.25352233Model URL (redirect): https://data.janelia.org/LN50OGithub repo: https://github.com/janelia-cellmap/cellmap-modelVisualization website: https://openorganelle.janelia.org/datasets/jrc_mus-thymus-1</p
Automatic nuclei segmentations in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of P7 mouse kidney (jrc_mus-kidney-3) model
No full textModel description: Cellpose 2.0 was trained on nuclei from 22 2D slices from jrc_mus-kidney-3.Architecture: Cellpose 2.0Input voxel size (nm): 128 x 128 x 128 (X, Y, Z)Output voxel size (nm): 128 x 128 x 128 (X, Y, Z)Classes trained on: NucleusGPU: NVIDIA TITAN RTXRAM: 768.0 GiBWall time (sec): 2198.31Software: Cellpose 2.0Software DOI: https://doi.org/10.1038/s41592-022-01663-4Source dataset (EM) ID: jrc_mus-kidney-3Source dataset (EM) DOI: https://doi.org/10.25378/janelia.24020799Generated dataset DOI: https://doi.org/10.25378/janelia.25352215Model URL (redirect): https://data.janelia.org/NXtm9Github repo: https://github.com/janelia-cellmap/cellmap-modelsVisualization website: https://openorganelle.janelia.org/datasets/jrc_mus-kidney-3</p
Automatic nuclei segmentations in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of P7 mouse pancreas (jrc_mus-pancreas-4) model
No full textModel description: Cellpose 2.0 was trained on nuclei from 17 2D slices from jrc_mus-pancreas-4.Architecture: Cellpose 2.0Input voxel size (nm): 128 x 128 x 128 (X, Y, Z)Output voxel size (nm): 128 x 128 x 128 (X, Y, Z)Classes trained on: NucleusGPU: RTX A6000RAM: 256.0 GiBSoftware: Cellpose 2.0Software DOI: https://doi.org/10.1038/s41592-022-01663-4Source dataset (EM) ID: jrc_mus-pancreas-4Source dataset (EM) DOI: https://doi.org/10.25378/janelia.23411843Generated dataset DOI: https://doi.org/10.25378/janelia.25352224Model URL (redirect): https://data.janelia.org/FThDpGithub repo: https://github.com/janelia-cellmap/cellmap-modelsVisualization website: https://openorganelle.janelia.org/datasets/jrc_mus-pancreas-4</p
Automatic vascular segmentations in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of P7 mouse heart (jrc_mus-heart-1) model
No full textModel description: Cellpose 2.0 was trained on extracellular space from 12 2D slices from jrc_mus-heart-1.
Architecture: Cellpose 2.0
Input voxel size (nm): 128 x 128 x 128 (X, Y, Z)
Output voxel size (nm): 128 x 128 x 128 (X, Y, Z)
Classes trained on: Extracellular space
GPU: NVIDIA TITAN RTX
RAM: 768.0 GiB
Wall time (sec): 2281.27
Software: Cellpose 2.0
Software DOI: https://doi.org/10.1038/s41592-022-01663-4
Source dataset (EM) ID: jrc_mus-heart-1
Source dataset (EM) DOI: https://doi.org/10.25378/janelia.24020919
Generated dataset DOI: https://doi.org/10.25378/janelia.25374010
Model URL (redirect): https://data.janelia.org/efZGR
Github repo: https://github.com/janelia-cellmap/cellmap-models
Visualization website: https://openorganelle.janelia.org/datasets/jrc_mus-heart-1</p
jrc_mus-sc-zp105a Ariadne.ai organelle segmentations
No full textOrganelle segmentations generated using Ariadne.ai, an automatic segmentation service applied to a FIB-SEM mouse spinal cord dataset subvolume.
Hereditary spastic paraplegias (HSPs) comprise a large group of inherited neurologic disorders affecting the longest corticospinal axons (SPG1–86 plus others), with shared manifestations of lower extremity spasticity and gait impairment. Common autosomal dominant HSPs are caused by mutations in genes encoding the microtubule-severing ATPase spastin (SPAST; SPG4), the membrane-bound GTPase atlastin-1 (ATL1; SPG3A) and the reticulon-like, microtubule-binding protein REEP1 (REEP1; SPG31). These proteins bind one another and function in shaping the tubular endoplasmic reticulum (ER) network. Typically, mouse models of HSPs have mild, later onset phenotypes, possibly reflecting far shorter lengths of their corticospinal axons relative to humans. Here, we have generated a robust, double mutant mouse model of HSP in which atlastin-1 is genetically modified with a K80A knock-in (KI) missense change that abolishes its GTPase activity, whereas its binding partner Reep1 is knocked out. Atl1KI/KI/Reep1−/− mice exhibit early onset and rapidly progressive declines in several motor function tests. Also, ER in mutant corticospinal axons dramatically expands transversely and periodically in a mutation dosage-dependent manner to create a ladder-like appearance, on the basis of reconstructions of focused ion beam-scanning electron microscopy datasets using machine learning-based auto-segmentation. In lockstep with changes in ER morphology, axonal mitochondria are fragmented and proportions of hypophosphorylated neurofilament H and M subunits are dramatically increased in Atl1KI/KI/Reep1−/− spinal cord. Co-occurrence of these findings links ER morphology changes to alterations in mitochondrial morphology and cytoskeletal organization. Atl1KI/KI/Reep1−/− mice represent an early onset rodent HSP model with robust behavioral and cellular readouts for testing novel therapies.
Sample:
Double-mutant ATL1 (knock-in) / REEP1 (knocked out), female, 6-month-old mouse dorsal corticospinal tract tissue
Protocol:
Mouse was anesthetized and transcardially perfused with 1× PBS followed by freshly made EM fixative (2% glutaraldehyde and 2% paraformaldehyde in 0.1 N cacodylate buffer). Spinal cord was removed and post-fixed in EM fixative overnight. Vibratome slices were treated with 0.2% OsO4 in phosphate buffer for 30 min, mordanted en bloc with 0.25% uranyl acetate overnight at 40°C, dehydrated with ethanol and embedded in Durcupan resin.
Contributions:
Sample provided by Craig Blackstone Lab (NINDS/NIH, currently at Harvard Medical School), prepared for imaging by Song Pang (HHMI/Janelia, currently at Yale School of Medicine), with imaging and post-processing by C. Shan Xu (HHMI/Janelia, currently at Yale School of Medicine).
Dataset ID: jrc_mus-sc-zp105a
EM Data DOI: 10.25378/janelia.20134979
EM voxel size (nm): 6.0 x 6.0 x 6.0 (X, Y, Z)
Segmentation voxel size (nm): 6.0 x 6.0 x 6.0 (X, Y, Z)
Dataset URL: https://data.janelia.org/B5muk
Visualization Website: https://openorganelle.janelia.org/datasets/jrc_mus-sc-zp105a
Segmented Organelles: ER, PM, Mito, Whole Cell</p
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