Sample Drift Correction Following 4D Confocal Time-lapse Imaging

Parslow, Adam C.; Cardona, Albert; Bryson-Richardson, Robert

doi:10.3791/51086-v

Cited by 23 publications

(17 citation statements)

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“…Registration was performed using a combination of the Fiji StackReg [ 62 ] and Correct 3D Drift plug‐ins. [ 63 ] A median filter was applied to despeckle and smooth the images, which were then inverted to make the chitinous material appear white and the Pt filling (corresponding to the air network) black. Segmentation was done using the trainable Weka segmentation 3D plug‐in [ 64 ] in Fiji.…”

Section: Methodsmentioning

confidence: 99%

3D Tomographic Analysis of the Order‐Disorder Interplay in the Pachyrhynchus congestus mirabilis Weevil

2022

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The bright colors of Pachyrhynchus weevils originate from complex dielectric nanostructures within their elytral scales. In contrast to previous work exhibiting highly ordered single‐network diamond‐type photonic crystals, here, it is shown by combining optical microscopy and spectroscopy measurements with 3D focused ion beam (FIB) tomography that the blue scales of P. congestus mirabilis differ from that of an ordered diamond structure. Through the use of FIB tomography on elytral scales filled with platinum (Pt) by electron beam‐assisted deposition, it is revealed that the red scales of this weevil possess a periodic diamond structure, while the network morphology of the blue scales exhibit diamond morphology only on the single scattering unit level with disorder on longer length scales. Full wave simulations performed on the reconstructed volumes indicate that this local order is sufficient to open a partial photonic bandgap even at low dielectric constant contrast between chitin and air in the absence of long‐range or translational order. The observation of disordered and ordered photonic crystals within a single organism opens up interesting questions on the cellular origin of coloration and studies on bio‐inspired replication of angle‐independent colors.

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Section: Methodsmentioning

confidence: 99%

3D Tomographic Analysis of the Order‐Disorder Interplay in the Pachyrhynchus congestus mirabilis Weevil

2022

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“…Briefly, the background signal was experimentally determined for each channel as a mean intensity in the blank image and subtracted from retinal images. The positional drift was corrected with the Correct 3D drift plug‐in 27 . Longitudinal view (XZ view) images were reconstructed from Z‐stack images.…”

Section: Methodsmentioning

confidence: 99%

Two‐photon AMPK and ATP imaging reveals the bias between rods and cones in glycolysis utility

Yamamoto

Sumiyama

et al. 2021

The FASEB Journal

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In vertebrates, retinal rod and cone photoreceptor cells rely significantly on glycolysis. Lactate released from photoreceptor cells fuels neighboring retinal pigment epithelium cells and Müller glial cells through oxidative phosphorylation. To understand this highly heterogeneous metabolic environment around photoreceptor cells, single-cell analysis is needed. Here, we visualized cellular AMP-activated protein kinase (AMPK) activity and ATP levels in the retina by two-photon microscopy. Transgenic mice expressing a hyBRET-AMPK biosensor were used for measuring the AMPK activity. GO-ATeam2 transgenic mice were used for measuring the ATP level. Temporal metabolic responses were successfully detected in the live retinal explants upon drug perfusion. A glycolysis inhibitor, 2-deoxy-d-glucose (2-DG), activated AMPK and reduced ATP. These effects were clearly stronger in rods than in cones. Notably, rod AMPK and ATP started to recover at 30 min from the onset of 2-DG perfusion. Consistent with these findings, ex vivo electroretinogram recordings showed a transient slowdown in rod dim flash responses during a 60-min 2-DG perfusion, whereas cone responses were not affected. Based on these results, we propose that cones surrounded by highly glycolytic rods become less dependent on glycolysis, and rods also become less dependent on glycolysis within 60 min upon the glycolysis inhibition.

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“…Only embryos that appeared healthy 24 hours post imaging were used for analysis. The tip of the notochord was used as a reference point to correct embryo drift in the Correct 3D direct ImageJ plugin (85). Embryos were handled similarly for imaging protrusions, except 15 confocal slices of 1µm thickness were collected every 1.5 min with a HC PL APO 40X/1.10 CS2 objective.…”

Section: Fluorescence Imagingmentioning

confidence: 99%

The myocardium utilizes Pdgfra-PI3K signaling to steer towards the midline during heart tube formation

Shrestha

McCann

Saravanan

et al. 2023

Preprint

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Coordinated cell movement is a fundamental process in organ formation. During heart development, bilateral myocardial precursors collectively move towards the midline (cardiac fusion) to form the primitive heart tube. Along with extrinsic influences such as the adjacent anterior endoderm which are known to be required for cardiac fusion, we previously showed that the platelet-derived growth factor receptor alpha (Pdgfra) is also required. However, an intrinsic mechanism that regulates myocardial movement remains to be elucidated. Here, we uncover an essential intrinsic role in the myocardium for the phosphoinositide 3-kinase (PI3K) intracellular signaling pathway in directing myocardial movement towards the midline. In vivo imaging reveals that in PI3K-inhibited zebrafish embryos myocardial movements are misdirected and slower, while midline-oriented dynamic myocardial membrane protrusions become unpolarized. Moreover, PI3K activity is dependent on and genetically interacts with Pdgfra to regulate myocardial movement. Together our findings reveal an intrinsic myocardial steering mechanism that responds to extrinsic cues during the initiation of cardiac development.

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Sample Drift Correction Following 4D Confocal Time-lapse Imaging

Cited by 23 publications

References 0 publications

3D Tomographic Analysis of the Order‐Disorder Interplay in the Pachyrhynchus congestus mirabilis Weevil

3D Tomographic Analysis of the Order‐Disorder Interplay in the Pachyrhynchus congestus mirabilis Weevil

Two‐photon AMPK and ATP imaging reveals the bias between rods and cones in glycolysis utility

The myocardium utilizes Pdgfra-PI3K signaling to steer towards the midline during heart tube formation

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