CLIJ: GPU-accelerated image processing for everyone

Haase, Robert; Royer, Loïc A.; Steinbach, Peter; Schmidt, Deborah; Dibrov, Alexandr; Weigert, Martin; Maghelli, Nicola; Tomančák, Pavel; Jug, Florian; Myers, Eugene W.

doi:10.1101/660704

Cited by 35 publications

(43 citation statements)

References 9 publications

(5 reference statements)

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“…For overlap analysis, Siglec channel intensities were multiplied by copies of the Iba1 and/or MHC-II masks that were dilated in 3D by 2 voxels to cover neighboring antibody signals. Voxel mask binary operations were performed using the And/Or/Not operations provided by ImageJ's CLIJ plugin (Haase et al, 2020). Mask overlap was calculated as Siglec∩IbaI Siglec for mask intensity and area values.…”

Section: Human Samplesmentioning

confidence: 99%

Phosphoproteomics identifies microglial Siglec‐F inflammatory response during neurodegeneration

Morshed

Ralvenius

Nott

et al. 2020

Molecular Systems Biology

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Alzheimer’s disease (AD) is characterized by the appearance of amyloid‐β plaques, neurofibrillary tangles, and inflammation in brain regions involved in memory. Using mass spectrometry, we have quantified the phosphoproteome of the CK‐p25, 5XFAD, and Tau P301S mouse models of neurodegeneration. We identified a shared response involving Siglec‐F which was upregulated on a subset of reactive microglia. The human paralog Siglec‐8 was also upregulated on microglia in AD. Siglec‐F and Siglec‐8 were upregulated following microglial activation with interferon gamma (IFNγ) in BV‐2 cell line and human stem cell‐derived microglia models. Siglec‐F overexpression activates an endocytic and pyroptotic inflammatory response in BV‐2 cells, dependent on its sialic acid substrates and immunoreceptor tyrosine‐based inhibition motif (ITIM) phosphorylation sites. Related human Siglecs induced a similar response in BV‐2 cells. Collectively, our results point to an important role for mouse Siglec‐F and human Siglec‐8 in regulating microglial activation during neurodegeneration.

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Section: Human Samplesmentioning

confidence: 99%

Phosphoproteomics identifies microglial Siglec‐F inflammatory response during neurodegeneration

Morshed

Ralvenius

Nott

et al. 2020

Molecular Systems Biology

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“…Arrival spaces may emerge and develop at different places across a city; their development depends on the overall housing market conditions and might change over time (Dunkl, Moldovan, & Leibert, 2019). We can identify different constellations or pathways of arrival spaces such as: a) "established, long-term" arrival spaces; b) areas where the arrival characteristics are being endangered by upgrading, displacement, and residential change; or c) areas where people move to due to a lack of alternatives (Haase & Schmidt, 2019). Arrival spaces thus may shift in terms of place, but they may also shift in meaning for the people living there.…”

Section: Urban Arrival Spaces: An Emerging Debatementioning

confidence: 99%

Leipzig’s Inner East as an Arrival Space? Exploring the Trajectory of a Diversifying Neighbourhood

Haase

Schmidt

Rink

et al. 2020

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The article analyses and discusses the development of Leipzig and especially its inner east as an ‘urban space of arrival’ since 1990. It represents a study about arrival in the post-socialist context that is fairly rare in the international debate so far, since most of the arrival debate builds on western European evidence. Leipzig’s inner east was characterised by shrinkage until the end of the 1990s and by new growth, especially after 2010, as the whole city grew. Since the second half of the 1990s the inner east has developed into a migrant area, referred to here as an ‘arrival space.’ Today, in 2020, it represents the most heterogeneous part of the city in terms of population structure and is one of the most dynamic areas in terms of in- and out-migration. At the same time, it represents an area where large amounts of the population face different types of disadvantage. Set against this context, the article embeds the story of Leipzig’s inner east into the arrival debate and investigates the area’s development according to the characteristics discussed by the debate. Our results reveal that Leipzig’s inner east represents a meaningful example of an arrival space in a specific (post-socialist, shrinkage followed by regrowth) context and that arrival and its spatial allocation strongly depend on factors like population, housing, and real estate market development, as well as policymaking and, significantly, recognition.

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“…Finally, altogether, while several years ago the amount of data obtained from 3D reconstructions would be significantly large and difficult to analyze, image analysis has advanced at increased speed over the past few years. Various tools now exist [ 44 – 46 ] that facilitate the analysis of large datasets such as the ones obtained in our work. We hope that the data presented here will hopefully inspire the development of whole-body imaging technologies to allow for the discovery of important host-pathogen interactions in the malaria field.…”

Section: Discussionmentioning

confidence: 99%

3D imaging of undissected optically cleared Anopheles stephensi mosquitoes and midguts infected with Plasmodium parasites

et al. 2020

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Malaria is a life-threatening disease, caused by Apicomplexan parasites of the Plasmodium genus. The Anopheles mosquito is necessary for the sexual replication of these parasites and for their transmission to vertebrate hosts, including humans. Imaging of the parasite within the insect vector has been attempted using multiple microscopy methods, most of which are hampered by the presence of the light scattering opaque cuticle of the mosquito. So far, most imaging of the Plasmodium mosquito stages depended on either sectioning or surgical dissection of important anatomical sites, such as the midgut and the salivary glands. Optical projection tomography (OPT) and light sheet fluorescence microscopy (LSFM) enable imaging fields of view in the centimeter scale whilst providing micrometer resolution. In this paper, we compare different optical clearing protocols and present reconstructions of the whole body of Plasmodium -infected, optically cleared Anopheles stephensi mosquitoes and their midguts. The 3D-reconstructions from OPT imaging show detailed features of the mosquito anatomy and enable overall localization of parasites in midguts. Additionally, LSFM imaging of mosquito midguts shows detailed distribution of oocysts in extracted midguts. This work was submitted as a pre-print to bioRxiv , available at https://www.biorxiv.org/content/10.1101/682054v2 .

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CLIJ: GPU-accelerated image processing for everyone

Cited by 35 publications

References 9 publications

Phosphoproteomics identifies microglial Siglec‐F inflammatory response during neurodegeneration

Phosphoproteomics identifies microglial Siglec‐F inflammatory response during neurodegeneration

Leipzig’s Inner East as an Arrival Space? Exploring the Trajectory of a Diversifying Neighbourhood

3D imaging of undissected optically cleared Anopheles stephensi mosquitoes and midguts infected with Plasmodium parasites

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