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jrc_mus-kidney organelle predictions

posted on 2023-04-07, 18:49 authored by CellMap Project TeamCellMap Project Team, Aubrey WeigelAubrey Weigel, David Ackerman, Davis Bennett, John BogovicJohn Bogovic, Alyson Petruncio, Larissa Heinrich, William Patton, Woohyun Park

 A collection of ground truth data, raw predictions, and refined predictions performed on a mouse kidney FIB-SEM dataset.

This dataset captures a region within the mouse renal cortex that includes several structures of physiological significance. The data set contains profiles of two glomeruli, which are situated towards the front and back ends of the image stack. Within each glomerulus are glomerular capillaries, podocyte epithelial cells and the cells of Bowman’s capsule. Both glomeruli are associated with profiles of their respective afferent and efferent arterioles. Juxtaglomular smooth muscle cells, laden with dense core secretory granules, can be seen in each of the two afferent arterioles. Each of the two glomeruli are associated with complete image sets of their immediately related juxtaglomeular apparati, including the associated macula densa cells. The data set contains extended profiles of two tubule types, which can be followed as they weave through the data set. The proximal convoluted tubules can be recognized by virtue of their apical brush borders, comprised of densely packed microvilli. The distal convoluted tubules lack apical brush borders and are instead endowed with deeply invaginated basolateral membranes that harbor long, vertically oriented mitochondria. Peritubular capillaries, lined by a single layer of endothelial cells, are found between all of the tubule profiles.

Understanding cellular architecture is essential for understanding biology. Electron microscopy (EM) uniquely visualizes cellular structure with nanometer resolution. However, traditional methods, such as thin-section EM or EM tomography, have limitations because they only visualize a single slice or a relatively small volume of the cell, respectively. We overcame these limitations by imaging whole cells and tissues via the enhanced focused ion beam scanning EM (FIB-SEM) platform at 8-nm voxels with week-long acquisition or 4-nm voxels with month-long acquisition. We used this approach to generate diverse reference 3D image datasets and hope to create a reference library to explore comprehensive quantification of whole cells and all their constituents. These open-access data offer a foundation upon which to nucleate a new volume of high-resolution whole-cell EM images and subsequent analyses, a new paradigm that invites biologists to explore and pose questions with a fresh perspective. 


Wild-type, 8 week old mouse, strain: C57BL/6 from Jackson Lab


Perfusion fixation with glutaraldehyde and vibratome section followed by room temperature reducing OTO staining. After dehydration and infiltration with graded ethanol and Durcupan resin, polymerize the sample in 60°C oven.


Region of Interest (ROI) and biology description provided by Michael J Caplan (Yale School of Medicine), sample provided by Wei-Ping Li (HHMI/Janelia), prepared for imaging by Song Pang (HHMI/Janelia), with imaging by Song Pang (HHMI/Janelia) and C. Shan Xu (HHMI/Janelia), post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia).

Dataset ID: jrc_mus-kidney

EM Data DOI: 10.25378/janelia.16913035

EM voxel size (nm): 8.0 x 8.0 x 8.0 (X, Y, Z)

Segmentation voxel size (nm): 8.0 x 8.0 x 8.0 (X, Y, Z)

Dataset URL: 

Visualization Website: https://openorganelle.janelia.org/datasets/jrc_mus-kidney 

Segmented Organelles: ER, Nucleus, PM, Mito, Mito mem

Included in Dataset: predictions, segmentations, ground truth