Orbit Image Analysis: An open-source whole slide image analysis tool

Stritt, Manuel; Stalder, Anna K.; Vezzali, Enrico

doi:10.1371/journal.pcbi.1007313

Cited by 94 publications

(48 citation statements)

References 41 publications

(45 reference statements)

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“…As shown in Fig 1A, perviousness was calculated as the difference in Hounsfield units, 16 in which larger differences indicate higher permeability. Cases were categorized as "high" or "low" perviousness based on a cutoff of the median perviousness across all cases in the dataset.…”

Section: Analysis Of Ctmentioning

confidence: 99%

Increased Perviousness on CT for Acute Ischemic Stroke is Associated with Fibrin/Platelet-Rich Clots

Patel

Fricano

Waqas

et al. 2020

AJNR Am J Neuroradiol

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BACKGROUND AND PURPOSE: Clot perviousness in acute ischemic stroke is a potential CT imaging biomarker for mechanical thrombectomy efficacy. We investigated the association among perviousness, clot cellular composition, and first-pass effect. MATERIALS AND METHODS: In 40 mechanical thrombectomy-treated cases of acute ischemic stroke, we calculated perviousness as the difference in clot density on CT angiography and noncontrast CT. We assessed the proportion of fibrin/platelet aggregates, red blood cells, and white blood cells on clot histopathology. We tested for linear correlation between histologic components and perviousness, differences in components between "high" and "low" pervious clots defined by median perviousness, and differences in perviousness/composition between cases that did and did not achieve a first-pass effect. RESULTS: Perviousness significantly positively and negatively correlated with the percentage of fibrin/platelet aggregates (P ¼ .001) and the percentage of red blood cells (P ¼ .001), respectively. Higher pervious clots had significantly greater fibrin/platelet aggregate content (P ¼ .042). Cases that achieved a first-pass effect (n ¼ 14) had lower perviousness, though not significantly (P ¼ .055). The percentage of red blood cells was significantly higher (P ¼ .028) and the percentage of fibrin/platelet aggregates was significantly lower (P ¼ .016) in cases with a first-pass effect. There was no association between clot density on NCCT and clot composition or first-pass effect. Receiver operating characteristic analysis indicated that clot composition was the best predictor of firstpass effect (area under receiver operating characteristic curve: percentage of fibrin/platelet aggregates ¼ 0.731, percentage of red blood cells ¼ 0.706, perviousness ¼ 0.668). CONCLUSIONS: Clot perviousness on CT is associated with a higher percentage of fibrin/platelet aggregate content. Histologic data and, to a lesser degree, perviousness may have value in predicting first-pass outcome. Imaging metrics that more strongly reflect clot biology than perviousness may be needed to predict a first-pass effect with high accuracy. ABBREVIATIONS: AIS ¼ acute ischemic stroke; AUC ¼ area under the curve; CV ¼ coefficient of variation; FP ¼ fibrin/platelet aggregates; FPE ¼ first-pass effect; MMI ¼ Mattes mutual information; MT ¼ mechanical thrombectomy; mTICI ¼ modified TICI; RBC ¼ red blood cells; ROC ¼ receiver operating characteristic; WBC ¼ white blood cells C T is the most common imaging technique used to evaluate patients with acute ischemic stroke (AIS). Together, NCCT and CTA can provide valuable information about the occlusive clot, such as its location, length, and density. 1-3 One parameter derived from these images is clot permeability, or perviousness, which indicates the amount of contrast that diffuses through the clot tissue. 1,4 Several clinical studies have claimed that perviousness may be an important indicator of how easily occlusive clots can be treated by tPA or mechanical thrombectomy (MT). 1...

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Section: Analysis Of Ctmentioning

confidence: 99%

Increased Perviousness on CT for Acute Ischemic Stroke is Associated with Fibrin/Platelet-Rich Clots

Patel

Fricano

Waqas

et al. 2020

AJNR Am J Neuroradiol

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“…Besides QuPath, whole-slide image analysis can be achieved with other open-source software, such as ImageJ [using the SlideJ plugin (Della Mea et al, 2017)], Orbit (Stritt et al, 2020), andIcy (de Chaumont et al, 2012). However, we are not aware of any studies comparing the reproducibility of the results, the time requirements for analysis or the ease of use among the three aforementioned software.…”

Section: Discussionmentioning

confidence: 99%

Whole-Slide Image Analysis of Human Pancreas Samples to Elucidate the Immunopathogenesis of Type 1 Diabetes Using the QuPath Software

Apaolaza

Πετροπούλου

Rodríguez-Calvo

2021

Front. Mol. Biosci.

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Type 1 diabetes is a chronic disease of the pancreas characterized by the loss of insulin-producing beta cells. Access to human pancreas samples for research purposes has been historically limited, restricting pathological analyses to animal models. However, intrinsic differences between animals and humans have made clinical translation very challenging. Recently, human pancreas samples have become available through several biobanks worldwide, and this has opened numerous opportunities for scientific discovery. In addition, the use of new imaging technologies has unraveled many mysteries of the human pancreas not merely in the presence of disease, but also in physiological conditions. Nowadays, multiplex immunofluorescence protocols as well as sophisticated image analysis tools can be employed. Here, we described the use of QuPath—an open-source platform for image analysis—for the investigation of human pancreas samples. We demonstrate that QuPath can be adequately used to analyze whole-slide images with the aim of identifying the islets of Langerhans and define their cellular composition as well as other basic morphological characteristics. In addition, we show that QuPath can identify immune cell populations in the exocrine tissue and islets of Langerhans, accurately localizing and quantifying immune infiltrates in the pancreas. Therefore, we present a tool and analysis pipeline that allows for the accurate characterization of the human pancreas, enabling the study of the anatomical and physiological changes underlying pancreatic diseases such as type 1 diabetes. The standardization and implementation of these analysis tools is of critical importance to understand disease pathogenesis, and may be informative for the design of new therapies aimed at preserving beta cell function and halting the inflammation caused by the immune attack.

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“…Osteopontin (OPN) and transforming growth factor β (TGF-β) (R&D Systems, Bio-Techne GmbH, Wiesbaden-Nordenstedt, Germany) stained lung tissue slides were photographed using a 25-fold magnification, and pictures were analyzed for positively stained areas in the lung tissue using the Software Orbit Image Analysis version 2.65 [Idorsia Pharmaceuticals Ltd., (67)]. Positively defined areas were calculated as percentage of the whole tissue lung section.…”

Section: Semiquantitative Analysis Of Lung Tissue Using Orbit Image Amentioning

confidence: 99%

Host CD39 Deficiency Affects Radiation-Induced Tumor Growth Delay and Aggravates Radiation-Induced Normal Tissue Toxicity

et al. 2020

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Orbit Image Analysis: An open-source whole slide image analysis tool

Cited by 94 publications

References 41 publications

Increased Perviousness on CT for Acute Ischemic Stroke is Associated with Fibrin/Platelet-Rich Clots

Increased Perviousness on CT for Acute Ischemic Stroke is Associated with Fibrin/Platelet-Rich Clots

Whole-Slide Image Analysis of Human Pancreas Samples to Elucidate the Immunopathogenesis of Type 1 Diabetes Using the QuPath Software

Host CD39 Deficiency Affects Radiation-Induced Tumor Growth Delay and Aggravates Radiation-Induced Normal Tissue Toxicity

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