Globally optimal stitching of tiled 3D microscopic image acquisitions

Preibisch, Stephan; Saalfeld, Stephan; Tomančák, Pavel

doi:10.1093/bioinformatics/btp184

Cited by 2,099 publications

(1,676 citation statements)

References 2 publications

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“…Following acquisition, a FIJI plugin 22 was used to stitch the images together based on OME-XML metadata. 23,24 Two-photon excited fluorescence images were also acquired without filtering in selected regions of interest.…”

Section: Multiphoton Microscopymentioning

confidence: 99%

Periductal stromal collagen topology of pancreatic ductal adenocarcinoma differs from that of normal and chronic pancreatitis

et al. 2015

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Pancreatic ductal adenocarcinoma continues to be one of the most difficult diseases to manage with one of the highest cancer mortality rates. This is due to several factors including nonspecific symptomatology and subsequent diagnosis at an advanced stage, aggressive metastatic behavior that is incompletely understood, and limited response to current therapeutic regimens. As in other cancers, there is great interest in studying the role of the tumor microenvironment in pancreatic ductal adenocarcinoma and whether components of this environment could serve as research and therapeutic targets. In particular, attention has turned toward the desmoplastic collagen-rich pancreatic ductal adenocarcinoma stroma for both biological and clinical insight. In this study, we used quantitative second harmonic generation microscopy to investigate stromal collagen organization and structure in human pancreatic ductal adenocarcinoma pathology tissues compared with non-neoplastic tissues. Collagen topology was characterized in whole-tissue microarray cores and at specific pathology-annotated epithelial-stroma interfaces representing 241 and 117 patients, respectively. We quantitatively demonstrate that a unique collagen topology exists in the periductal pancreatic ductal adenocarcinoma stroma. Specifically, collagen around malignant ducts shows increased alignment, length, and width compared with normal ducts and benign ducts in a chronic pancreatitis background. These findings indicate that second harmonic generation imaging can provide quantitative information about fibrosis that complements traditional histopathologic insights and can serve as a rich field for investigation into pathogenic and clinical implications of reorganized collagen as a pancreatic ductal adenocarcinoma disease marker. Pancreatic ductal adenocarcinoma is one of the most devastating human malignancies. It is currently the fourth leading cause of cancer death and projects to become the second leading cause by 2030. 1 The 5-year relative survival rate has remained in the single digits for decades. Pancreatic ductal adenocarcinoma is notoriously difficult to detect before an advanced, inoperable stage is reached due to nonspecific symptomatology and the retroperitoneal location of the pancreas, which makes palpation or routine biopsy of suspicious masses difficult. Recent advances in the sensitivity and specificity of preoperative imaging modalities such as computer tomography, magnetic resonance imaging, positron emission tomography, endoscopic ultrasonography, and endoscopic retrograde cholangiopancreatography have played an important role in enhancing pancreatic ductal adenocarcinoma diagnosis, detailing the relationship of lesions to nearby anatomical structures, and determining the course of management. 2 Despite these advances, only 10-15% of patients are diagnosed at a localized disease stage when surgical resection is possible as a potential curative therapy. However, postsurgical recurrence rates are high with 5-year survival rate of

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Section: Multiphoton Microscopymentioning

confidence: 99%

Periductal stromal collagen topology of pancreatic ductal adenocarcinoma differs from that of normal and chronic pancreatitis

et al. 2015

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“…To obtain image sequences in which single cells could be tracked over the length of the experiments the imaging data were restructured using Fiji image processing software. 28,29 All raw images for each channel (Hoechst, YFP or PI) were opened as image sequence and brightness and contrast were adjusted. The nine adjacent fields of views (512 × 512 pixel) which were imaged with a 13% overlap at each time point were combined together into a 1432 × 1432 pixel image using the 'Stitch Sequence of Grids of Images' plugin.…”

mentioning

confidence: 99%

“…The nine adjacent fields of views (512 × 512 pixel) which were imaged with a 13% overlap at each time point were combined together into a 1432 × 1432 pixel image using the 'Stitch Sequence of Grids of Images' plugin. 28,29 CellProfiler 2.0 image analysis software 30 was used to analyse mean YFP intensity and percentage of PI positive cells of the whole cell population in these image sequences (see below). For single cell traces, cells were randomly chosen and tracked manually starting at the latest frame by defining a region of interest around the object, which was adjusted for each frame to accommodate cell movement.…”

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confidence: 99%

Imaging of single cell responses to ER stress indicates that the relative dynamics of IRE1/XBP1 and PERK/ATF4 signalling rather than a switch between signalling branches determine cell survival

et al. 2015

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An accumulation of misfolded proteins in the endoplasmic reticulum (ER) triggers the unfolded protein response (UPR) mediated via the activation of three transmembrane proteins IRE1, PERK and ATF6. Signalling through these proteins is aimed at enhancing the ER folding capacity and reducing the folding load. If these processes fail to re-establish protein homeostasis within the ER, then cell death prevails via apoptosis. How the shift from pro-survival to pro-apoptotic signalling is regulated remains unclear with both IRE1 and PERK signalling associated with pro-survival as well as pro-apoptotic signalling. To investigate the temporal activation of IRE1 and PERK in live cells and their relationship to cellular fate, we devised single cell reporters for both ER stress signalling branches. SH-SY5Y neural cells stably expressing these fluorescent protein reporter constructs to monitor IRE1-splicing activity and PERK-mediated ATF4-translation were imaged using single cell and high content time lapse live cell microscopy. We could correlate an early onset and attenuation of XBP1 splicing in the IRE1-reporter cells as cytoprotective. Indeed, silencing of IRE1 expression using shRNA inhibited splicing of XBP1 resulting in an early onset of cell death. In contrast, in the PERK-reporter cells, we observed that a slow rate of ATF4-translation and late re-initiation of general translation coincided with cells which were resistant to ER stress-induced cell death. Interestingly, whereas silencing of PERK did not affect overall levels of cell death in response to ER stress, it did increase sensitivity to ER stressors at early time points following treatment. Our results suggest that apoptosis activation in response to ER stress is not caused by a preferential activation of a single UPR branch, or by a switch from one branch to the other. Rather, our data indicated that the relative timing of IRE1 and PERK signalling determines the shift from cell survival to apoptosis.

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“…As mentioned above, the injections were imaged with a confocal fluorescent microscope under a protected atmosphere (22 °C, > 85% humidity) to prevent drying of the samples. Finally, the image tiles were reconstructed using an open-source plugin [32].…”

Section: Lift For Direct Three-dimensional Liquid Deliverymentioning

confidence: 99%

Depth-controlled laser-induced jet injection for direct three-dimensional liquid delivery

et al. 2018

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Needle-free jet injection enables the delivery of drugs into skin or soft tissue by puncturing them with a high-velocity liquid jet. However, precise and efficient drug delivery requires generating such liquid jets with both a controlled velocity and a high throughput, which remains challenging with current spring-and gas-actuated jet injectors. Here, we propose a depth-controlled and high-throughput injection method by adapting laser-induced forward transfer (LIFT), a high-resolution two-dimensional printing technique, for direct three-dimensional liquid delivery into soft tissues.The velocity of thin liquid jets is laser actuated from 10 to 85 m/s so that doses as small as 10 pL, not achievable with other injectors, are injected at a 1 Hz repetition rate into a 300 μm thick soft gelatin substrate with a 25 μm depth precision and 12 μm lateral resolution. We further investigate the potential of this liquid delivery technique as a direct three-dimensional cell-delivery vehicle and show that depth-controlled particle delivery requires high-delivery efficiency. Our direct three-dimensional liquid delivery system opens up more possibilities for pinpoint drug delivery in soft tissues or tissue-engineered constructs.

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Globally optimal stitching of tiled 3D microscopic image acquisitions

Cited by 2,099 publications

References 2 publications

Periductal stromal collagen topology of pancreatic ductal adenocarcinoma differs from that of normal and chronic pancreatitis

Periductal stromal collagen topology of pancreatic ductal adenocarcinoma differs from that of normal and chronic pancreatitis

Imaging of single cell responses to ER stress indicates that the relative dynamics of IRE1/XBP1 and PERK/ATF4 signalling rather than a switch between signalling branches determine cell survival

Depth-controlled laser-induced jet injection for direct three-dimensional liquid delivery

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