imaris 3d watershedding algorithm Search Results


3d connected region counting  (Oxford Instruments)
99
Oxford Instruments 3d connected region counting
Overview of the workflow for assessing the density of neurons. (A) The mouse brain is imaged using two modalities: MRH imaging while the brain is in the skull, followed by LSM after the brain is removed from the skull and subjected to tissue clearing. (B) The LSM data are pre-processed by registering to MRH correcting the deformation in brain morphology. (C) The automated workflow locates the region with the label from r1CCFv3 and generates random subvolumes within that region to sample, applying the design-based principles of optical fractionation. Neurons in each subvolume are identified via a random forest algorithm followed by <t>3D</t> <t>watershed</t> and volume filters and counted.
3d Connected Region Counting, supplied by Oxford Instruments, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/imaris+3d+watershedding+algorithm/Imaris/pmc10569694-138-5-17
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3d connected region counting - by Bioz Stars, 2026-09
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Overview of the workflow for assessing the density of neurons. (A) The mouse brain is imaged using two modalities: MRH imaging while the brain is in the skull, followed by LSM after the brain is removed from the skull and subjected to tissue clearing. (B) The LSM data are pre-processed by registering to MRH correcting the deformation in brain morphology. (C) The automated workflow locates the region with the label from r1CCFv3 and generates random subvolumes within that region to sample, applying the design-based principles of optical fractionation. Neurons in each subvolume are identified via a random forest algorithm followed by 3D watershed and volume filters and counted.

Journal: Frontiers in Neuroscience

Article Title: A rapid workflow for neuron counting in combined light sheet microscopy and magnetic resonance histology

doi: 10.3389/fnins.2023.1223226

Figure Lengend Snippet: Overview of the workflow for assessing the density of neurons. (A) The mouse brain is imaged using two modalities: MRH imaging while the brain is in the skull, followed by LSM after the brain is removed from the skull and subjected to tissue clearing. (B) The LSM data are pre-processed by registering to MRH correcting the deformation in brain morphology. (C) The automated workflow locates the region with the label from r1CCFv3 and generates random subvolumes within that region to sample, applying the design-based principles of optical fractionation. Neurons in each subvolume are identified via a random forest algorithm followed by 3D watershed and volume filters and counted.

Article Snippet: The watershed method and the 3D connected region counting method in the first algorithm are available in Imaris.

Techniques: Imaging, Fractionation