Challenges and Practical Solutions to MRI and Histology Matching and Measurements Using Available ImageJ Software Tools
Traditionally histology is the gold standard for the validation of imaging experiments. Matching imaging slices and histological sections and the precise outlining of corresponding tissue structures are difficult. Challenges are based on differences in imaging and histological slice thickness as wel...
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| Format: | Article |
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MDPI AG
2022-06-01
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| Series: | Biomedicines |
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| Online Access: | https://www.mdpi.com/2227-9059/10/7/1556 |
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| author | Marina Y. Khodanovich Tatyana V. Anan’ina Elena P. Krutenkova Andrey E. Akulov Marina S. Kudabaeva Mikhail V. Svetlik Yana A. Tumentceva Maria M. Shadrina Anna V. Naumova |
| author_facet | Marina Y. Khodanovich Tatyana V. Anan’ina Elena P. Krutenkova Andrey E. Akulov Marina S. Kudabaeva Mikhail V. Svetlik Yana A. Tumentceva Maria M. Shadrina Anna V. Naumova |
| author_sort | Marina Y. Khodanovich |
| collection | DOAJ |
| description | Traditionally histology is the gold standard for the validation of imaging experiments. Matching imaging slices and histological sections and the precise outlining of corresponding tissue structures are difficult. Challenges are based on differences in imaging and histological slice thickness as well as tissue shrinkage and alterations after processing. Here we describe step-by-step instructions that might be used as a universal pathway to overlay MRI and histological images and for a correlation of measurements between imaging modalities. The free available (Fiji is just) ImageJ software tools were used for regions of interest transformation (ROIT) and alignment using a rat brain MRI as an example. The developed ROIT procedure was compared to a manual delineation of rat brain structures. The ROIT plugin was developed for ImageJ to enable an automatization of the image processing and structural analysis of the rodent brain. |
| first_indexed | 2024-03-09T03:40:26Z |
| format | Article |
| id | doaj.art-6f1b4eb8490c4abf81ba12ef3c2f365f |
| institution | Directory Open Access Journal |
| issn | 2227-9059 |
| language | English |
| last_indexed | 2024-03-09T03:40:26Z |
| publishDate | 2022-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomedicines |
| spelling | doaj.art-6f1b4eb8490c4abf81ba12ef3c2f365f2023-12-03T14:41:33ZengMDPI AGBiomedicines2227-90592022-06-01107155610.3390/biomedicines10071556Challenges and Practical Solutions to MRI and Histology Matching and Measurements Using Available ImageJ Software ToolsMarina Y. Khodanovich0Tatyana V. Anan’ina1Elena P. Krutenkova2Andrey E. Akulov3Marina S. Kudabaeva4Mikhail V. Svetlik5Yana A. Tumentceva6Maria M. Shadrina7Anna V. Naumova8Laboratory of Neurobiology, Research Institute of Biology and Biophysics, Tomsk State University, Russia. 36, Lenina Ave., 634050 Tomsk, RussiaLaboratory of Neurobiology, Research Institute of Biology and Biophysics, Tomsk State University, Russia. 36, Lenina Ave., 634050 Tomsk, RussiaLaboratory of Neurobiology, Research Institute of Biology and Biophysics, Tomsk State University, Russia. 36, Lenina Ave., 634050 Tomsk, RussiaInstitute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 10 Lavrentyeva Avenue, 630090 Novosibirsk, RussiaLaboratory of Neurobiology, Research Institute of Biology and Biophysics, Tomsk State University, Russia. 36, Lenina Ave., 634050 Tomsk, RussiaLaboratory of Neurobiology, Research Institute of Biology and Biophysics, Tomsk State University, Russia. 36, Lenina Ave., 634050 Tomsk, RussiaLaboratory of Neurobiology, Research Institute of Biology and Biophysics, Tomsk State University, Russia. 36, Lenina Ave., 634050 Tomsk, RussiaLaboratory of Neurobiology, Research Institute of Biology and Biophysics, Tomsk State University, Russia. 36, Lenina Ave., 634050 Tomsk, RussiaLaboratory of Neurobiology, Research Institute of Biology and Biophysics, Tomsk State University, Russia. 36, Lenina Ave., 634050 Tomsk, RussiaTraditionally histology is the gold standard for the validation of imaging experiments. Matching imaging slices and histological sections and the precise outlining of corresponding tissue structures are difficult. Challenges are based on differences in imaging and histological slice thickness as well as tissue shrinkage and alterations after processing. Here we describe step-by-step instructions that might be used as a universal pathway to overlay MRI and histological images and for a correlation of measurements between imaging modalities. The free available (Fiji is just) ImageJ software tools were used for regions of interest transformation (ROIT) and alignment using a rat brain MRI as an example. The developed ROIT procedure was compared to a manual delineation of rat brain structures. The ROIT plugin was developed for ImageJ to enable an automatization of the image processing and structural analysis of the rodent brain.https://www.mdpi.com/2227-9059/10/7/1556magnetic resonance imagingMRIhistologyimmunofluorescencequantificationregistration |
| spellingShingle | Marina Y. Khodanovich Tatyana V. Anan’ina Elena P. Krutenkova Andrey E. Akulov Marina S. Kudabaeva Mikhail V. Svetlik Yana A. Tumentceva Maria M. Shadrina Anna V. Naumova Challenges and Practical Solutions to MRI and Histology Matching and Measurements Using Available ImageJ Software Tools Biomedicines magnetic resonance imaging MRI histology immunofluorescence quantification registration |
| title | Challenges and Practical Solutions to MRI and Histology Matching and Measurements Using Available ImageJ Software Tools |
| title_full | Challenges and Practical Solutions to MRI and Histology Matching and Measurements Using Available ImageJ Software Tools |
| title_fullStr | Challenges and Practical Solutions to MRI and Histology Matching and Measurements Using Available ImageJ Software Tools |
| title_full_unstemmed | Challenges and Practical Solutions to MRI and Histology Matching and Measurements Using Available ImageJ Software Tools |
| title_short | Challenges and Practical Solutions to MRI and Histology Matching and Measurements Using Available ImageJ Software Tools |
| title_sort | challenges and practical solutions to mri and histology matching and measurements using available imagej software tools |
| topic | magnetic resonance imaging MRI histology immunofluorescence quantification registration |
| url | https://www.mdpi.com/2227-9059/10/7/1556 |
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