DiAna, an ImageJ tool for object-based 3D co-localization and distance analysis

Gilles, Jean-François; Santos, Marc Dos; Boudier, Thomas; Bolte, Susanne; Heck, Nicolas

doi:10.1016/j.ymeth.2016.11.016

Cited by 163 publications

(145 citation statements)

References 40 publications

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“…S3C and S3D). To confirm the existence of a non-random spatial relationship, we carried out random shuffle nearest neighbour analysis on IFNγ-treated NPCs (36). Actual distances between HLA-B spots and PML bodies were observed to be significantly shorter than simulated distances following randomisation (P < 0.0001), confirming a positive spatial relationship (Fig.…”

Section: Ifnγ Induces Hla-b Transcription Near Pml Nuclear Bodiesmentioning

confidence: 72%

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Antiviral signalling in human IPSC-derived neurons recapitulates neurodevelopmental disorder phenotypes

Warre-Cornish

Perfect

Nagy

et al. 2019

Preprint

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Maternal immune activation increases the risk of neurodevelopmental disorders.Elevated cytokines, such as interferon-gamma (IFNγ), in offspring's brains play a central role. IFNγ activates an antiviral cellular state, limiting viral entry and replication. In addition, IFNγ has been implicated in brain development. Here, we hypothesise that IFNγ-induced antiviral signalling contributes to molecular and cellular phenotypes associated with neurodevelopmental disorders. We find that transient IFNγ treatment of neural progenitors derived from human induced pluripotent stem cells (hIPSCs) persistently increases neurite outgrowth, phenocopying hIPSC-neurons from autistic individuals. IFNγ upregulates antiviral PML bodies and MHC class I (MHCI) genes, which persists through neuronal differentiation. Critically, IFNγ-induced neurite outgrowth requires both PML and MHCI. We also find that IFNγ disproportionately alters expression of autism and schizophrenia risk genes, suggesting convergence between these genetic and environmental risk factors. Together, these data indicate that IFNγ-induced antiviral signalling may contribute to neurodevelopmental disorder aetiology. PMLNormalised expression * *

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Section: Ifnγ Induces Hla-b Transcription Near Pml Nuclear Bodiesmentioning

confidence: 72%

“…Confocal images were taken with a Leica SP5 laser scanning confocal microscope, DiAna, an Image J Plugin (36), was used to assess the spatial distribution of objects.…”

Section: Microscopy and Image Analysismentioning

confidence: 99%

Antiviral signalling in human IPSC-derived neurons recapitulates neurodevelopmental disorder phenotypes

Warre-Cornish

Perfect

Nagy

et al. 2019

Preprint

View full text Add to dashboard Cite

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“…All images were processed using Image J (Fiji) and Imaris software for 3D reconstruction. For colocalization and synapse number analysis, data were processed with ImageJ Distance Analysis (DiAna) plugin (22).…”

Section: Immunohistochemistry and Image Analysismentioning

confidence: 99%

CDC50A dependent phosphatidylserine exposure induces inhibitory post-synapse elimination by microglia

Park

Jung

Lee

et al. 2020

Preprint

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Glia contribute to synapse elimination through phagocytosis in the central nervous system. Despite important roles during development and neurological disorders, the "eat-me" signal that initiates glia-mediated phagocytosis of synapses remains largely elusive. Here, by generating inducible conditional knockout mice of Cdc50a, we induced stable exposure of phosphatidylserine in the neuronal outer membrane. Surprisingly, acute Cdc50a deletion in neurons causes specific loss of inhibitory post-synapses without affecting other synapses, thereby generating excessive excitability with appearance of seizure. Ablating microglia or deleting microglial Mertk rescues the loss of inhibitory post-synapses, indicating that microglial phagocytosis is responsible for inhibitory post-synapse elimination. Moreover, inhibitory post-synapses in normal juvenile brains also use phosphatidylserine for synapse pruning by microglia, suggesting that phosphatidylserine may serve as a general "eat-me" signal for inhibitory post-synapse elimination. One Sentence SummaryCdc50a dependent phosphatidylserine exposure functions as an "eat-me" signal for microgliadependent inhibitory post-synapse elimination

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“…A region of interest was manually traced in each mosaic to define the area in which axons were segmented and counted. Segmentation was performed in three-dimensions (3D) by iterative thresholding and MESR algorithm 28,29 . User-defined constraints (i.e.…”

Section: Quantification Of Labelled Corticospinal Axons In the White mentioning

confidence: 99%

Loss of floor plate Netrin-1 impairs midline crossing of corticospinal axons and leads to mirror movements

Pourchet

Morel

Welniarz

et al. 2020

Preprint

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In human, execution of unimanual movements requires lateralized activation of the primary motor cortex, which then transmits the motor command to the contralateral hand through the crossed corticospinal tract (CST). Mutations in NETRIN-1 alter motor control lateralization, leading to congenital mirror movements. To address the role of midline Netrin-1 on CST development and subsequent motor control, we analyzed the morphological and functional consequences of floor-plate Netrin-1 depletion in conditional knock-out mice (Shh::cre;Ntn1 lox/lox mice). Here, we show that depletion of floor plate Netrin-1 critically disrupts midline crossing of the CST, whereas the other commissural systems are mostly preserved. The CST defect results in abnormal but functional ipsilateral projections, and is associated with abnormal symmetric movements. Therefore, our study reveals a new role for Netrin-1 in CST development. It also describes a unique mouse model recapitulating characteristics of human congenital mirror movements, through abnormal CST decussation.

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DiAna, an ImageJ tool for object-based 3D co-localization and distance analysis

Cited by 163 publications

References 40 publications

Antiviral signalling in human IPSC-derived neurons recapitulates neurodevelopmental disorder phenotypes

Antiviral signalling in human IPSC-derived neurons recapitulates neurodevelopmental disorder phenotypes

CDC50A dependent phosphatidylserine exposure induces inhibitory post-synapse elimination by microglia

Loss of floor plate Netrin-1 impairs midline crossing of corticospinal axons and leads to mirror movements

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