Challenges and Practical Solutions to MRI and Histology Matching and Measurements Using Available ImageJ Software Tools

Khodanovich, M. Yu.; Anan’ina, T. V.; Krutenkova, Elena; Akulov, Andrey E.; Kudabaeva, Marina S; Svetlik, M. V.; Tumentceva, Yana A; Shadrina, Maria M; Naumova, Anna V.

doi:10.3390/biomedicines10071556

Cited by 4 publications

(3 citation statements)

References 46 publications

(83 reference statements)

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“…[ 42 ] A particularly powerful mesoscale imaging modality for this endeavor is MRI, especially when combined with microscale imaging modalities, for instance LM. [ 43 , 44 ] This combination mandates the presence of MRI‐contrast in the sample and its transparency for light to penetrate the sample. Nevertheless, prior to this report, the prevailing consensus maintained that optically‐cleared specimens, particularly those subjected to the CLARITY method, are deemed unfit for MRI.…”

Section: Discussionmentioning

confidence: 99%

Revealing the MRI‐Contrast in Optically Cleared Brains

Oz,

Saar,

Olszakier

et al. 2024

Advanced Science

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The current consensus holds that optically‐cleared specimens are unsuitable for Magnetic Resonance Imaging (MRI); exhibiting absence of contrast. Prior studies combined MRI with tissue‐clearing techniques relying on the latter's ability to eliminate lipids, thereby fostering the assumption that lipids constitute the primary source of ex vivo MRI‐contrast. Nevertheless, these findings contradict an extensive body of literature that underscores the contribution of other features to contrast. Furthermore, it remains unknown whether non‐delipidating clearing methods can produce MRI‐compatible specimens or whether MRI‐contrast can be re‐established. These limitations hinder the development of multimodal MRI‐light‐microscopy (LM) imaging approaches. This study assesses the relation between MRI‐contrast, and delipidation in optically‐cleared whole brains following different tissue‐clearing approaches. It is demonstrated that uDISCO and ECi‐brains are MRI‐compatible upon tissue rehydration, despite both methods’ substantial delipidating‐nature. It is also demonstrated that, whereas Scale‐clearing preserves most lipids, Scale‐cleared brain lack MRI‐contrast. Furthermore, MRI‐contrast is restored to lipid‐free CLARITY‐brains without introducing lipids. Our results thereby dissociate between the essentiality of lipids to MRI‐contrast. A tight association is found between tissue expansion, hyperhydration and loss of MRI‐contrast. These findings then enabled us to develop a multimodal MRI‐LM‐imaging approach, opening new avenues to bridge between the micro‐ and mesoscale for biomedical research and clinical applications.

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Section: Discussionmentioning

confidence: 99%

Revealing the MRI‐Contrast in Optically Cleared Brains

Oz,

Saar,

Olszakier

et al. 2024

Advanced Science

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“…These stained slices were observed and photographed using a digital trinocular camera microscope BA410-Digital (Motic China Group Co. Ltd., Xiamen, China). According to the methods described in several previous studies ( 19 – 21 ), the goose splenic histological paraments were analyzed using Image-Pro Plus 6.0 software (National Institutes of Health, Bethesda, MD).…”

Section: Methodsmentioning

confidence: 99%

Effects of cage vs. net-floor mixed rearing system on goose spleen histomorphology and gene expression profiles

Chen,

Song,

et al. 2024

Front. Vet. Sci.

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Due to the demands for both environmental protection and modernization of the goose industry in China, the traditional goose waterside rearing systems have been gradually transitioning to the modern intensive dryland rearing ones, such as the net-floor mixed rearing system (MRS) and cage rearing system (CRS). However, the goose immune responses to different dryland rearing systems remain poorly understood. This study aimed to investigate and compare the age-dependent effects of MRS and CRS on the splenic histomorphological characteristics and immune-related genes expression profiles among three economically important goose breeds, including Sichuan White goose (SW), Gang goose (GE), and Landes goose (LD). Morphological analysis revealed that the splenic weight and organ index of SW were higher under CRS than under MRS (p < 0.05). Histological observations showed that for SW and LD, the splenic corpuscle diameter and area as well as trabecular artery diameter were larger under MRS than under CRS at 30 or 43 weeks of age (p < 0.05), while the splenic red pulp area of GE was larger under CRS than under MRS at 43 weeks of age (p < 0.05). Besides, at 43 weeks of age, higher mRNA expression levels of NGF, SPI1, and VEGFA in spleens of SW were observed under MRS than under CRS (p < 0.05), while higher levels of HSPA2 and NGF in spleens of LD were observed under MRS than under CRS (p < 0.05). For GE, there were higher mRNA expression levels of MYD88 in spleens under CRS at 30 weeks of age (p < 0.05). Moreover, our correlation analysis showed that there appeared to be more pronounced positive associations between the splenic histological parameters and expression levels of several key immune-related genes under MRS than under CRS. Therefore, it is speculated that the geese reared under MRS might exhibit enhanced immune functions than those under CRS, particularly for SW and LD. Although these phenotypic differences are assumed to be associated with the age-dependent differential expression profiles of HSPA2, MYD88, NGF, SPI1, and VEGFA in the goose spleen, the underlying regulatory mechanisms await further investigations.

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“…Im-ageJ is an easy-to-use tool that has become popular for analyzing and measuring scientific images. Some users have used ImageJ to perform cell size analysis, histology, and immunohistochemistry (9,(13)(14)(15)(16).…”

Section: Introductionmentioning

confidence: 99%

Digital Image Analysis of Diabetic Foot Ulcer Areas Using ImageJ Software (National Institute of Health, USA) in Patients Treated with Autologous Activated Platelet-rich Plasma Injection

2023

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Background: In this cross-sectional study, we investigated three diabetic foot ulcer (DFU) patients. DFU is a serious diabetes complication affecting general health and social life. Autologous regenerative therapies, such as autologous activated platelet-rich plasma (aaPRP), have been proposed for DFU management. However, precise instruments are required to measure the wound size to evaluate wound closure after treatment. Objectives: This study aimed to evaluate the DFU healing process treated by aaPRP through digital image analysis using ImageJ software (National Institute of Health, USA). Methods: The DFU patients were administered aaPRP and followed up on days 7 and 14. The healing process was analyzed through ImageJ software. Paired t-test was used to assess the wound healing process. Results: The results showed that ImageJ was useful for wound area measurement. Granulation and sloughy tissue development can be evaluated and calculated as a part of wound healing progress. Conclusions: We conclude that ImageJ facilitates DFU analysis not only about the size but also on the healing time process through visualization of granulation and sloughy tissue formation, which can represent the healing progress.

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Challenges and Practical Solutions to MRI and Histology Matching and Measurements Using Available ImageJ Software Tools

Cited by 4 publications

References 46 publications

Revealing the MRI‐Contrast in Optically Cleared Brains

Revealing the MRI‐Contrast in Optically Cleared Brains

Effects of cage vs. net-floor mixed rearing system on goose spleen histomorphology and gene expression profiles

Digital Image Analysis of Diabetic Foot Ulcer Areas Using ImageJ Software (National Institute of Health, USA) in Patients Treated with Autologous Activated Platelet-rich Plasma Injection

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