Manual and Semi-Automated Measurement and Calculation of Osteosarcoma Treatment Effect Using Whole Slide Image and Qupath
Introduction: In osteosarcoma, the most significant indicator of prognosis is the histologic changes related to tumor response to preoperative chemotherapy, such as necrosis. We have developed a method to measure the osteosarcoma treatment effect using whole slide image (WSI) with an open-source dig...
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| Veröffentlicht in: | Pediatric and developmental pathology 2024-01, Vol.27 (1), p.32-38 |
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| container_title | Pediatric and developmental pathology |
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| creator | He, Mai He, Bofan Weng, Jinyi Cheng, Jerry Q. Gu, Huanying |
| description | Introduction:
In osteosarcoma, the most significant indicator of prognosis is the histologic changes related to tumor response to preoperative chemotherapy, such as necrosis. We have developed a method to measure the osteosarcoma treatment effect using whole slide image (WSI) with an open-source digital image analytical software Qupath.
Materials and Methods:
In Qupath, each osteosarcoma case was treated as a project. All H&E slides from the entire representative slice of osteosarcoma were scanned into WSIs and imported into a project in Qupath. The regions of tumor and tumor necrosis were annotated, and their areas were measured in Qupath. In order to measure the osteosarcoma treatment effect, we needed to calculate the percentage of total necrosis area over total tumor area. We developed a tool that can automatically extract all values of tumor and necrosis areas from a Qupath project into an Excel file, sum these values for necrosis and whole tumor respectively, and calculate necrosis/tumor percentage.
Conclusion:
Our method that combines WSI with Qupath can provide an objective measurement to facilitate pathologist’s assessment of osteosarcoma response to treatment. The proposed approach can also be used for other types of tumors that have clinical need for post-treatment response assessment. |
| doi_str_mv | 10.1177/10935266231207937 |
| format | Article |
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In osteosarcoma, the most significant indicator of prognosis is the histologic changes related to tumor response to preoperative chemotherapy, such as necrosis. We have developed a method to measure the osteosarcoma treatment effect using whole slide image (WSI) with an open-source digital image analytical software Qupath.
Materials and Methods:
In Qupath, each osteosarcoma case was treated as a project. All H&E slides from the entire representative slice of osteosarcoma were scanned into WSIs and imported into a project in Qupath. The regions of tumor and tumor necrosis were annotated, and their areas were measured in Qupath. In order to measure the osteosarcoma treatment effect, we needed to calculate the percentage of total necrosis area over total tumor area. We developed a tool that can automatically extract all values of tumor and necrosis areas from a Qupath project into an Excel file, sum these values for necrosis and whole tumor respectively, and calculate necrosis/tumor percentage.
Conclusion:
Our method that combines WSI with Qupath can provide an objective measurement to facilitate pathologist’s assessment of osteosarcoma response to treatment. The proposed approach can also be used for other types of tumors that have clinical need for post-treatment response assessment.</description><identifier>ISSN: 1093-5266</identifier><identifier>EISSN: 1615-5742</identifier><identifier>DOI: 10.1177/10935266231207937</identifier><identifier>PMID: 37943723</identifier><language>eng</language><publisher>Los Angeles, CA: SAGE Publications</publisher><subject>Bone Neoplasms - diagnosis ; Bone Neoplasms - pathology ; Bone Neoplasms - therapy ; Humans ; Necrosis - pathology ; Osteosarcoma - diagnosis ; Osteosarcoma - pathology ; Osteosarcoma - therapy ; Software</subject><ispartof>Pediatric and developmental pathology, 2024-01, Vol.27 (1), p.32-38</ispartof><rights>2023, Society for Pediatric Pathology All rights reserved</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c292t-444d873bcfb46ee5177d691487e9e48daf7826ab106b017e63091ae2e3cc6f63</cites><orcidid>0000-0002-4775-9757</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://journals.sagepub.com/doi/pdf/10.1177/10935266231207937$$EPDF$$P50$$Gsage$$H</linktopdf><linktohtml>$$Uhttps://journals.sagepub.com/doi/10.1177/10935266231207937$$EHTML$$P50$$Gsage$$H</linktohtml><link.rule.ids>315,781,785,21824,27929,27930,43626,43627</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/37943723$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>He, Mai</creatorcontrib><creatorcontrib>He, Bofan</creatorcontrib><creatorcontrib>Weng, Jinyi</creatorcontrib><creatorcontrib>Cheng, Jerry Q.</creatorcontrib><creatorcontrib>Gu, Huanying</creatorcontrib><title>Manual and Semi-Automated Measurement and Calculation of Osteosarcoma Treatment Effect Using Whole Slide Image and Qupath</title><title>Pediatric and developmental pathology</title><addtitle>Pediatr Dev Pathol</addtitle><description>Introduction:
In osteosarcoma, the most significant indicator of prognosis is the histologic changes related to tumor response to preoperative chemotherapy, such as necrosis. We have developed a method to measure the osteosarcoma treatment effect using whole slide image (WSI) with an open-source digital image analytical software Qupath.
Materials and Methods:
In Qupath, each osteosarcoma case was treated as a project. All H&E slides from the entire representative slice of osteosarcoma were scanned into WSIs and imported into a project in Qupath. The regions of tumor and tumor necrosis were annotated, and their areas were measured in Qupath. In order to measure the osteosarcoma treatment effect, we needed to calculate the percentage of total necrosis area over total tumor area. We developed a tool that can automatically extract all values of tumor and necrosis areas from a Qupath project into an Excel file, sum these values for necrosis and whole tumor respectively, and calculate necrosis/tumor percentage.
Conclusion:
Our method that combines WSI with Qupath can provide an objective measurement to facilitate pathologist’s assessment of osteosarcoma response to treatment. The proposed approach can also be used for other types of tumors that have clinical need for post-treatment response assessment.</description><subject>Bone Neoplasms - diagnosis</subject><subject>Bone Neoplasms - pathology</subject><subject>Bone Neoplasms - therapy</subject><subject>Humans</subject><subject>Necrosis - pathology</subject><subject>Osteosarcoma - diagnosis</subject><subject>Osteosarcoma - pathology</subject><subject>Osteosarcoma - therapy</subject><subject>Software</subject><issn>1093-5266</issn><issn>1615-5742</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kElLxEAUhBtR3H-AF-mjl2hv050cZXADRcQRj-Gl86KRJD32cvDf286oF8HTe1BfFVQRcsTZKefGnHFWyZnQWkgumKmk2SC7XPNZMTNKbOY_68UXsEP2QnhjLJs02yY70lRKGiF3yccdTAkGClNLH3Hsi_MU3QgRW3qHEJLHEae4kucw2DRA7N1EXUfvQ0QXwNuM04VHiCvyouvQRvoU-umFPr-6Aenj0LdIb0Z4wVXQQ1pCfD0gWx0MAQ-_7z5ZXF4s5tfF7f3Vzfz8trCiErFQSrWlkY3tGqURZ7lCqyuuSoMVqrKFzpRCQ8OZbnI_1JJVHFCgtFZ3Wu6Tk3Xs0rv3hCHWYx8sDgNM6FKoRVlWQpZaqIzyNWq9C8FjVy99P4L_qDmrvwav_wyePcff8akZsf11_CycgdM1EHL9-s0lP-W2_yR-Aqn1iMI</recordid><startdate>202401</startdate><enddate>202401</enddate><creator>He, Mai</creator><creator>He, Bofan</creator><creator>Weng, Jinyi</creator><creator>Cheng, Jerry Q.</creator><creator>Gu, Huanying</creator><general>SAGE Publications</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-4775-9757</orcidid></search><sort><creationdate>202401</creationdate><title>Manual and Semi-Automated Measurement and Calculation of Osteosarcoma Treatment Effect Using Whole Slide Image and Qupath</title><author>He, Mai ; He, Bofan ; Weng, Jinyi ; Cheng, Jerry Q. ; Gu, Huanying</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c292t-444d873bcfb46ee5177d691487e9e48daf7826ab106b017e63091ae2e3cc6f63</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Bone Neoplasms - diagnosis</topic><topic>Bone Neoplasms - pathology</topic><topic>Bone Neoplasms - therapy</topic><topic>Humans</topic><topic>Necrosis - pathology</topic><topic>Osteosarcoma - diagnosis</topic><topic>Osteosarcoma - pathology</topic><topic>Osteosarcoma - therapy</topic><topic>Software</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>He, Mai</creatorcontrib><creatorcontrib>He, Bofan</creatorcontrib><creatorcontrib>Weng, Jinyi</creatorcontrib><creatorcontrib>Cheng, Jerry Q.</creatorcontrib><creatorcontrib>Gu, Huanying</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Pediatric and developmental pathology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>He, Mai</au><au>He, Bofan</au><au>Weng, Jinyi</au><au>Cheng, Jerry Q.</au><au>Gu, Huanying</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Manual and Semi-Automated Measurement and Calculation of Osteosarcoma Treatment Effect Using Whole Slide Image and Qupath</atitle><jtitle>Pediatric and developmental pathology</jtitle><addtitle>Pediatr Dev Pathol</addtitle><date>2024-01</date><risdate>2024</risdate><volume>27</volume><issue>1</issue><spage>32</spage><epage>38</epage><pages>32-38</pages><issn>1093-5266</issn><eissn>1615-5742</eissn><abstract>Introduction:
In osteosarcoma, the most significant indicator of prognosis is the histologic changes related to tumor response to preoperative chemotherapy, such as necrosis. We have developed a method to measure the osteosarcoma treatment effect using whole slide image (WSI) with an open-source digital image analytical software Qupath.
Materials and Methods:
In Qupath, each osteosarcoma case was treated as a project. All H&E slides from the entire representative slice of osteosarcoma were scanned into WSIs and imported into a project in Qupath. The regions of tumor and tumor necrosis were annotated, and their areas were measured in Qupath. In order to measure the osteosarcoma treatment effect, we needed to calculate the percentage of total necrosis area over total tumor area. We developed a tool that can automatically extract all values of tumor and necrosis areas from a Qupath project into an Excel file, sum these values for necrosis and whole tumor respectively, and calculate necrosis/tumor percentage.
Conclusion:
Our method that combines WSI with Qupath can provide an objective measurement to facilitate pathologist’s assessment of osteosarcoma response to treatment. The proposed approach can also be used for other types of tumors that have clinical need for post-treatment response assessment.</abstract><cop>Los Angeles, CA</cop><pub>SAGE Publications</pub><pmid>37943723</pmid><doi>10.1177/10935266231207937</doi><tpages>7</tpages><orcidid>https://orcid.org/0000-0002-4775-9757</orcidid></addata></record> |
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| subjects | Bone Neoplasms - diagnosis Bone Neoplasms - pathology Bone Neoplasms - therapy Humans Necrosis - pathology Osteosarcoma - diagnosis Osteosarcoma - pathology Osteosarcoma - therapy Software |
| title | Manual and Semi-Automated Measurement and Calculation of Osteosarcoma Treatment Effect Using Whole Slide Image and Qupath |
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