Fiji: an open-source platform for biological-image analysis

Schindelin, Johannes; Arganda‐Carreras, Ignacio; Frise, Erwin; Kaynig, Verena; Longair, Mark; Pietzsch, Tobias; Preibisch, Stephan; Rueden, Curtis; Saalfeld, Stephan; Schmid, Benjamin; Tinévez, Jean-Yves; White, Daniel J.; Hartenstein, Volker; Eliceiri, Kevin W.; Tomančák, Pavel; Cardona, Albert

doi:10.1038/nmeth.2019

Cited by 54,084 publications

(44,426 citation statements)

References 52 publications

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“…Time lapse movies were acquired at a frequency of 1 frame every 10 s for 20 h and saved as Motion JPEG using a MATLAB (The MathWorks, Inc., Natick, MA) script. Movie post-processing (cropping, concatenation, resizing, addition of scale bar) was done using MATLAB and Fiji 27 . All MATLAB scripts written for this study are available upon request.…”

Section: Methodsmentioning

confidence: 99%

Paternal chromosome loss and metabolic crisis contribute to hybrid inviability in Xenopus

Gibeaux

Acker

Kitaoka

et al. 2018

Nature

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Section: Methodsmentioning

confidence: 99%

Paternal chromosome loss and metabolic crisis contribute to hybrid inviability in Xenopus

Gibeaux

Acker

Kitaoka

et al. 2018

Nature

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“…Analysis of confocal images was performed using pre-existing plugins or custom-designed macros in the Fiji distribution of the ImageJ software [96], supplemented by calculations in Excel (Microsoft). Details of the macros are available upon request.…”

Section: Methodsmentioning

confidence: 99%

Drosophila Rab2 controls endosome-lysosome fusion and LAMP delivery to late endosomes

2018

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Rab2 is a conserved Rab GTPase with a well-established role in secretory pathway function and phagocytosis. Here we demonstrate that Drosophila Rab2 is recruited to late endosomal membranes, where it controls the fusion of LAMP-containing biosynthetic carriers and lysosomes to late endosomes. In contrast, the lysosomal GTPase Gie/Arl8 is only required for late endosome-lysosome fusion, but not for the delivery of LAMP to the endocytic pathway. We also find that Rab2 is required for the fusion of autophagosomes to the endolysosomal pathway, but not for the biogenesis of lysosome-related organelles. Surprisingly, Rab2 does not rely on HOPS-mediated vesicular fusion for recruitment to late endosomal membranes. Our work suggests that Drosophila Rab2 is a central regulator of the endolysosomal and macroautophagic/autophagic pathways by controlling the major heterotypic fusion processes at the late endosome.

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“…Computer-assisted quantification of CD8+ signal was performed by setting a common threshold for all the images by using Fiji software. 79 …”

Section: Methodsmentioning

confidence: 99%

Inhibition of RON kinase potentiates anti-CTLA-4 immunotherapy to shrink breast tumors and prevent metastatic outgrowth

et al. 2018

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The advent of immune checkpoint blockade as a new strategy for immunotherapy has changed the outlook for many aggressive cancers. Although complete tumor eradication is attainable in some cases, durable clinical responses are observed only in a small fraction of patients, underlining urgent need for improvement. We previously showed that RON, a receptor tyrosine kinase expressed in macrophages, suppresses antitumor immune responses, and facilitates progression and metastasis of breast cancer. Here, we investigated the molecular changes that occur downstream of RON activation in macrophages, and whether inhibition of RON can cooperate with checkpoint immunotherapy to eradicate tumors. Activation of RON by its ligand, MSP, altered the gene expression profile of macrophages drastically and upregulated surface levels of CD80 and PD-L1, ligands for T-cell checkpoint receptors CTLA-4 and PD-1. Genetic deletion or pharmacological inhibition of RON in combination with anti-CTLA-4, but not with anti-PD-1, resulted in improved clinical responses against orthotopically transplanted tumors compared to single-agent treatment groups, resulting in complete tumor eradication in 46% of the animals. Positive responses to therapy were associated with higher levels of T-cell activation markers and tumor-infiltrating lymphocytes. Importantly, co-inhibition of RON and anti-CTLA-4 was also effective in clearing metastatic breast cancer cells in lungs, resulting in clinical responses in nearly 60% of the mice. These findings suggest that RON inhibition can be a novel approach to potentiate responses to checkpoint immunotherapy in breast cancer.

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Fiji: an open-source platform for biological-image analysis

Cited by 54,084 publications

References 52 publications

Paternal chromosome loss and metabolic crisis contribute to hybrid inviability in Xenopus

Paternal chromosome loss and metabolic crisis contribute to hybrid inviability in Xenopus

Drosophila Rab2 controls endosome-lysosome fusion and LAMP delivery to late endosomes

Inhibition of RON kinase potentiates anti-CTLA-4 immunotherapy to shrink breast tumors and prevent metastatic outgrowth

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