MosaicIA: an ImageJ/Fiji plugin for spatial pattern and interaction analysis

Shivanandan, Arun; Radenović, Aleksandra; Sbalzarini, Ivo F.

doi:10.1186/1471-2105-14-349

Cited by 83 publications

(69 citation statements)

References 18 publications

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“…While the photophysical properties of the probes, labeling and imaging strategies make image analysis complex, with adequate care, it is possible to measure protein stoichiometry (multimeric, dimeric or oligomeric) [43,46], count protein numbers [30,42,44,47,48] and characterize the spatial nano-organization of proteins [33,49]. A number of open-source (typically ImageJ-based) software is now available for biologists who wish to quantify their super-resolution images [24,37]. As the field moves forward, researchers will greatly benefit from the development of new probes or identification of buffer and imaging conditions that lead to high photon outputs, high photoactivation efficiencies and low blinking or re-activation rates.…”

Section: Discussionmentioning

confidence: 99%

“…In this case, multiple appearance of the same probe does not influence the cross-correlation curve, making analysis and interpretation easier. Spatial co-organization and co-localization of proteins can also be quantified by determining an "interaction potential" that is most likely to lead to the observed distribution of point localizations [36,37].…”

Section: Artificial Clustering and Over-countingmentioning

confidence: 99%

See 1 more Smart Citation

Quantitative super-resolution microscopy: pitfalls and strategies for image analysis

Durisic

Laparra-Cuervo

Lakadamyali

2014

Current Opinion in Chemical Biology

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Super-resolution microscopy is an enabling technology that allows biologists to visualize cellular structures at nanometer length scales using far-field optics. To break the diffraction barrier, it is necessary to leverage the distinct molecular states of fluorescent probes. At the same time, the existence of these different molecular states and the photophysical properties of the fluorescent probes can complicate data quantification and interpretation. Here, we review the pitfalls in super-resolution data analysis that must be avoided for proper interpretation of images.

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Section: Discussionmentioning

confidence: 99%

Section: Artificial Clustering and Over-countingmentioning

confidence: 99%

Quantitative super-resolution microscopy: pitfalls and strategies for image analysis

Durisic

Laparra-Cuervo

Lakadamyali

2014

Current Opinion in Chemical Biology

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“…4B. Identification of EB1 comets in the absence of nucleating sites was done with the MOSAIC plugin (35) for ImageJ. Some images were acquired on the same setup in which the Andor Neo sCMOS camera was used instead.…”

Section: Methodsmentioning

confidence: 99%

Microtubule nucleation remote from centrosomes may explain how asters span large cells

Ishihara

Nguyen

Groen

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

119

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A major challenge in cell biology is to understand how nanometersized molecules can organize micrometer-sized cells in space and time. One solution in many animal cells is a radial array of microtubules called an aster, which is nucleated by a central organizing center and spans the entire cytoplasm. Frog (here Xenopus laevis) embryos are more than 1 mm in diameter and divide with a defined geometry every 30 min. Like smaller cells, they are organized by asters, which grow, interact, and move to precisely position the cleavage planes. It has been unclear whether asters grow to fill the enormous egg by the same mechanism used in smaller somatic cells, or whether special mechanisms are required. We addressed this question by imaging growing asters in a cell-free system derived from eggs, where asters grew to hundreds of microns in diameter. By tracking marks on the lattice, we found that microtubules could slide outward, but this was not essential for rapid aster growth. Polymer treadmilling did not occur. By measuring the number and positions of microtubule ends over time, we found that most microtubules were nucleated away from the centrosome and that interphase egg cytoplasm supported spontaneous nucleation after a time lag. We propose that aster growth is initiated by centrosomes but that asters grow by propagating a wave of microtubule nucleation stimulated by the presence of preexisting microtubules.aster | centrosome | microtubule nucleation | embryo | Xenopus

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“…Because the images in STORM data represent a reconstruction of locations and localization uncertainties of individual molecules, the overlap of signal in images is not the best method for determining whether molecules colocalize. Instead, we used a nearest-neighbor analysis to determine how close each point source is to its nearest neighbor by using the "strength" metric (69,70). Supporting the hypothesis of microdomain mixing, we found that, upon Snx1/2 depletion, the interaction strength between RME-8 and Hrs increased significantly [3.33 (n = 3) compared with 1.13 (n = 3) for control; P < 0.02, t test; Fig.…”

Section: Not All Retromer Associated Proteins Are Important For Domainmentioning

confidence: 99%

SNX-1 and RME-8 oppose the assembly of HGRS-1/ESCRT-0 degradative microdomains on endosomes

Norris

Tammineni

Wang

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

100

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After endocytosis, transmembrane cargo reaches endosomes, where it encounters complexes dedicated to opposing functions: recycling and degradation. Microdomains containing endosomal sorting complexes required for transport (ESCRT)-0 component Hrs [hepatocyte growth factor-regulated tyrosine kinase substrate (HGRS-1) in Caenorhabditis elegans] mediate cargo degradation, concentrating ubiquitinated cargo and organizing the activities of ESCRT. At the same time, retromer associated sorting nexin one (SNX-1) and its binding partner, J-domain protein RME-8, sort cargo away from degradation, promoting cargo recycling to the Golgi. Thus, we hypothesized that there could be important regulatory interactions between retromer and ESCRT that balance degradative and recycling functions. Taking advantage of the naturally large endosomes of the C. elegans coelomocyte, we visualized complementary ESCRT-0 and RME-8/SNX-1 microdomains in vivo and assayed the ability of retromer and ESCRT microdomains to regulate one another. We found in snx-1(0) and rme-8(ts) mutants increased endosomal coverage and intensity of HGRS-1-labeled microdomains, as well as increased total levels of HGRS-1 bound to membranes. These effects are specific to SNX-1 and RME-8, as loss of other retromer components SNX-3 and vacuolar protein sorting-associated protein 35 (VPS-35) did not affect HGRS-1 microdomains. Additionally, knockdown of hgrs-1 had little to no effect on SNX-1 and RME-8 microdomains, suggesting directionality to the interaction. Separation of the functionally distinct ESCRT-0 and SNX-1/RME-8 microdomains was also compromised in the absence of RME-8 and SNX-1, a phenomenon we observed to be conserved, as depletion of Snx1 and Snx2 in HeLa cells also led to greater overlap of Rme-8 and Hrs on endosomes.endosome | SNX-1 | RME-8 | Hrs | clathrin

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MosaicIA: an ImageJ/Fiji plugin for spatial pattern and interaction analysis

Cited by 83 publications

References 18 publications

Quantitative super-resolution microscopy: pitfalls and strategies for image analysis

Quantitative super-resolution microscopy: pitfalls and strategies for image analysis

Microtubule nucleation remote from centrosomes may explain how asters span large cells

SNX-1 and RME-8 oppose the assembly of HGRS-1/ESCRT-0 degradative microdomains on endosomes

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