The ImageJ ecosystem: An open platform for biomedical image analysis

Schindelin, Johannes; Rueden, Curtis; Hiner, Mark; Eliceiri, Kevin W.

doi:10.1002/mrd.22489

Cited by 2,533 publications

(2,075 citation statements)

References 35 publications

(32 reference statements)

Supporting

Mentioning

2,057

Contrasting

Unclassified

Order By: Relevance

“…During the third week of flowering, one flower from the main raceme of each plant was selected when the petal laminae were perpendicular to the style and petals (mean: 2.0, Table S3) were carefully removed from the flower. The petals were affixed to transparency film with clear tape, scanned at 600 dpi, and the petal areas were calculated using imagej Version 1.44 (Schindelin et al ., 2015). …”

Section: Methodsmentioning

confidence: 99%

Oilseed rape (Brassica napus) as a resource for farmland insect pollinators: quantifying floral traits in conventional varieties and breeding systems

et al. 2017

View full text Add to dashboard Cite

Oilseed rape (OSR; Brassica napus L.) is a major crop in temperate regions and provides an important source of nutrition to many of the yield‐enhancing insect flower visitors that consume floral nectar. The manipulation of mechanisms that control various crop plant traits for the benefit of pollinators has been suggested in the bid to increase food security, but little is known about inherent floral trait expression in contemporary OSR varieties or the breeding systems used in OSR breeding programmes. We studied a range of floral traits in glasshouse‐grown, certified conventional varieties of winter OSR to test for variation among and within breeding systems. We measured 24‐h nectar secretion rate, amount, concentration and ratio of nectar sugars per flower, and sizes and number of flowers produced per plant from 24 varieties of OSR representing open‐pollinated (OP), genic male sterility (GMS) hybrid and cytoplasmic male sterility (CMS) hybrid breeding systems. Sugar concentration was consistent among and within the breeding systems; however, GMS hybrids produced more nectar and more sugar per flower than CMS hybrid or OP varieties. With the exception of ratio of fructose/glucose in OP varieties, we found that nectar traits were consistent within all the breeding systems. When scaled, GMS hybrids produced 1.73 times more nectar resource per plant than OP varieties. Nectar production and amount of nectar sugar in OSR plants were independent of number and size of flowers. Our data show that floral traits of glasshouse‐grown OSR differed among breeding systems, suggesting that manipulation and enhancement of nectar rewards for insect flower visitors, including pollinators, could be included in future OSR breeding programmes.

show abstract

Section: Methodsmentioning

confidence: 99%

Oilseed rape (Brassica napus) as a resource for farmland insect pollinators: quantifying floral traits in conventional varieties and breeding systems

et al. 2017

View full text Add to dashboard Cite

show abstract

“…Individual images of 512 × 512 pixels were acquired within the constraints of the grid with a 10% overlap between images. 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

View full text Add to dashboard Cite

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

show abstract

“…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%

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

View full text Add to dashboard Cite

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.

show abstract

The ImageJ ecosystem: An open platform for biomedical image analysis

Cited by 2,533 publications

References 35 publications

Oilseed rape (Brassica napus) as a resource for farmland insect pollinators: quantifying floral traits in conventional varieties and breeding systems

Oilseed rape (Brassica napus) as a resource for farmland insect pollinators: quantifying floral traits in conventional varieties and breeding systems

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

Contact Info

Product

Resources

About