Isolating specific cell and tissue compartments from 3D images for quantitative regional distribution analysis using novel computer algorithms.
BACKGROUND
Isolating specific cellular and tissue compartments from 3D image stacks for quantitative distribution analysis is crucial for understanding cellular and tissue physiology under normal and pathological conditions. Current approaches are limited because they are designed to map the distributions of synapses onto the dendrites of stained neurons and/or require specific proprietary software packages for their implementation.


METHODS
To overcome these obstacles, we developed algorithms to Grow and Shrink Volumes of Interest (GSVI) to isolate specific cellular and tissue compartments from 3D image stacks for quantitative analysis and incorporated these algorithms into a user-friendly computer program that is open source and downloadable at no cost.


RESULTS
The GSVI algorithm was used to isolate perivascular regions in the cortex of live animals and cell membrane regions of stained spinal motoneurons in histological sections. We tracked the real-time, intravital biodistribution of injected fluorophores with sub-cellular resolution from the vascular lumen to the perivascular and parenchymal space following a vascular microlesion, and mapped the precise distributions of membrane-associated KCC2 and gephyrin immunolabeling in dendritic and somatic regions of spinal motoneurons.


METHODS
Compared to existing approaches, the GSVI approach is specifically designed for isolating perivascular regions and membrane-associated regions for quantitative analysis, is user-friendly, and free.


CONCLUSIONS
The GSVI algorithm is useful to quantify regional differences of stained biomarkers (e.g., cell membrane-associated channels) in relation to cell functions, and the effects of therapeutic strategies on the redistributions of biomolecules, drugs, and cells in diseased or injured tissues.
CIHR Group in Sensory-Motor Integration, Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada K7L 3N6; Center for Neuroscience Studies, Queen's University, Kingston, ON, Canada K7L 3N6; Aix Marseille University, Developmental Biology Institute of Marseille-Luminy (IBDML), CNRS 7288, Case 907 - Parc Scientifique de Luminy, 13009 Marseille, France; Faculty of Rehabilitation Medicine, University of Alberta, 3-88 Corbett Hall, Edmonton, AB, Canada T6G 2G4. Electronic address: fenrich@ualberta.ca.
Keith K
KK
Fenrich
CIHR Group in Sensory-Motor Integration, Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada K7L 3N6; Center for Neuroscience Studies, Queen's University, Kingston, ON, Canada K7L 3N6.
Ethan Y
EY
Zhao
CIHR Group in Sensory-Motor Integration, Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada K7L 3N6; Center for Neuroscience Studies, Queen's University, Kingston, ON, Canada K7L 3N6.
Yuan
Y
Wei
CIHR Group in Sensory-Motor Integration, Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada K7L 3N6; Center for Neuroscience Studies, Queen's University, Kingston, ON, Canada K7L 3N6.
Anirudh
A
Garg
CIHR Group in Sensory-Motor Integration, Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada K7L 3N6; Center for Neuroscience Studies, Queen's University, Kingston, ON, Canada K7L 3N6. Electronic address: ken.rose@queensu.ca.
P Ken
PK
Rose
D000465:Algorithms; D000818:Animals; D002352:Carrier Proteins / Q000378:metabolism; D002415:Cats; D002462:Cell Membrane / Q000378:metabolism; D002540:Cerebral Cortex / Q000033:anatomy & histology* / Q000098:blood supply / Q000166:cytology*; D002561:Cerebrovascular Disorders / Q000473:pathology; D002574:Cervical Vertebrae; D003712:Dendrites / Q000378:metabolism; D005260:Female; D005455:Fluorescent Antibody Technique / Q000379:methods; D021621:Imaging, Three-Dimensional / Q000379:methods*; D033181:Information Dissemination; D008565:Membrane Proteins / Q000378:metabolism; D018613:Microscopy, Confocal / Q000379:methods; D009046:Motor Neurons / Q000166:cytology* / Q000378:metabolism; D061848:Optical Imaging; D012984:Software; D013116:Spinal Cord / Q000166:cytology* / Q000378:metabolism; D027981:Symporters / Q000378:metabolism; D013997:Time Factors; D000096922:K Cl- Cotransporters
D002352:Carrier Proteins; D008565:Membrane Proteins; D027981:Symporters; D000096922:K Cl- Cotransporters; C073441:gephyrin
Image analysis; Intravital microscopy; Membrane proteins; Open-source