{"data":{"id":"10.24433/co.9888828.v2","type":"dois","attributes":{"doi":"10.24433/co.9888828.v2","prefix":"10.24433","suffix":"co.9888828.v2","identifiers":[{"identifier":"fae6f7d3-5b73-4370-805f-384fabd7154b","identifierType":"Code Ocean ID"},{"identifier":"1545326","identifierType":"Code Ocean Slug"}],"alternateIdentifiers":[{"alternateIdentifierType":"Code Ocean ID","alternateIdentifier":"fae6f7d3-5b73-4370-805f-384fabd7154b"},{"alternateIdentifierType":"Code Ocean Slug","alternateIdentifier":"1545326"}],"creators":[{"name":"Dashan Dong","affiliation":["Boston University"],"nameIdentifiers":[]},{"name":"Danchen Jia","affiliation":["Boston University"],"nameIdentifiers":[]},{"name":"Xinyan Teng","affiliation":["Boston University"],"nameIdentifiers":[]},{"name":"Jianpeng Ao","affiliation":["Boston University"],"nameIdentifiers":[]},{"name":"Abu-Aqil, George","nameType":"Personal","givenName":"George","familyName":"Abu-Aqil","affiliation":["Boston University"],"nameIdentifiers":[]},{"name":"Biwen Gao","affiliation":["Boston University"],"nameIdentifiers":[]},{"name":"Zhang, Meng","nameType":"Personal","givenName":"Meng","familyName":"Zhang","affiliation":["Boston University"],"nameIdentifiers":[]},{"name":"Xia, Qing","nameType":"Personal","givenName":"Qing","familyName":"Xia","affiliation":["Boston University"],"nameIdentifiers":[]},{"name":"Ji-Xin Cheng","affiliation":["Boston University"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"Chem-SIM: Super-resolution Chemical Imaging via Photothermal Modulation of Structured-Illumination Fluorescence"}],"publisher":"Code Ocean","container":{},"publicationYear":2026,"subjects":[{"subject":"Capsule"},{"subject":"Biology"}],"contributors":[],"dates":[{"date":"2026-05-16","dateType":"Accepted"},{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"COMP","bibtex":"misc","citeproc":"article","schemaOrg":"SoftwareSourceCode","resourceType":"Capsule","resourceTypeGeneral":"Software"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":"2.0","rightsList":[{"rights":"MIT License","rightsUri":"https://opensource.org/licenses/MIT","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"mit","rightsIdentifierScheme":"SPDX"},{"rights":"No Rights Reserved (CC0)","rightsUri":"https://creativecommons.org/share-your-work/public-domain/cc0/"}],"descriptions":[{"description":"The capsule focuses on two modules used in Chem-SIM:\n\n**P-MLD (Poisson Maximum-Likelihood Demodulation)**\n\nA statistically grounded demodulation method for structured-illumination photothermal modulation data. P-MLD models the paired Hot/Cold photon-count measurements under a forward SIM modulation model and estimates modulation-amplitude images via Poisson maximum-likelihood fitting. This approach is designed to improve robustness in photon-limited regimes and to reduce artifacts that can arise from conventional differencing-based demodulation.\n\n**specNorm (Spectral Normalization):**\n\nA hyperspectral normalization workflow that stabilizes Chem-SIM spectra across wavenumbers and helps decouple chemical contrast from fluorescence brightness variations. specNorm performs intensity referencing and spectral scaling to yield consistent, comparable spectra across pixels and across wavelengths.","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"PD94bWwgdmVyc2lvbj0iMS4wIiBlbmNvZGluZz0iVVRGLTgiPz4KPHJlc291cmNlIHhtbG5zPSJodHRwOi8vZGF0YWNpdGUub3JnL3NjaGVtYS9rZXJuZWwtNCIgeG1sbnM6X1hNTFNjaGVtYS1pbnN0YW5jZT0iaHR0cDovL3d3dy53My5vcmcvMjAwMS9YTUxTY2hlbWEtaW5zdGFuY2UiIF9YTUxTY2hlbWEtaW5zdGFuY2U6c2NoZW1hTG9jYXRpb249Imh0dHA6Ly9kYXRhY2l0ZS5vcmcvc2NoZW1hL2tlcm5lbC00IGh0dHA6Ly9zY2hlbWEuZGF0YWNpdGUub3JnL21ldGEva2VybmVsLTQvbWV0YWRhdGEueHNkIj4KICA8aWRlbnRpZmllciBpZGVudGlmaWVyVHlwZT0iRE9JIj4xMC4yNDQzMy9DTy45ODg4ODI4LlYyPC9pZGVudGlmaWVyPgogIDxjcmVhdG9ycz4KICAgIDxjcmVhdG9yPgogICAgICA8Y3JlYXRvck5hbWU+RGFzaGFuIERvbmc8L2NyZWF0b3JOYW1lPgogICAgICA8YWZmaWxpYXRpb24+Qm9zdG9uIFVuaXZlcnNpdHk8L2FmZmlsaWF0aW9uPgogICAgPC9jcmVhdG9yPgogICAgPGNyZWF0b3I+CiAgICAgIDxjcmVhdG9yTmFtZT5EYW5jaGVuIEppYTwvY3JlYXRvck5hbWU+CiAgICAgIDxhZmZpbGlhdGlvbj5Cb3N0b24gVW5pdmVyc2l0eTwvYWZmaWxpYXRpb24+CiAgICA8L2NyZWF0b3I+CiAgICA8Y3JlYXRvcj4KICAgICAgPGNyZWF0b3JOYW1lPlhpbnlhbiBUZW5nPC9jcmVhdG9yTmFtZT4KICAgICAgPGFmZmlsaWF0aW9uPkJvc3RvbiBVbml2ZXJzaXR5PC9hZmZpbGlhdGlvbj4KICAgIDwvY3JlYXRvcj4KICAgIDxjcmVhdG9yPgogICAgICA8Y3JlYXRvck5hbWU+SmlhbnBlbmcgQW88L2NyZWF0b3JOYW1lPgogICAgICA8YWZmaWxpYXRpb24+Qm9zdG9uIFVuaXZlcnNpdHk8L2FmZmlsaWF0aW9uPgogICAgPC9jcmVhdG9yPgogICAgPGNyZWF0b3I+CiAgICAgIDxjcmVhdG9yTmFtZT5HZW9yZ2UgQWJ1LUFxaWw8L2NyZWF0b3JOYW1lPgogICAgICA8YWZmaWxpYXRpb24+Qm9zdG9uIFVuaXZlcnNpdHk8L2FmZmlsaWF0aW9uPgogICAgPC9jcmVhdG9yPgogICAgPGNyZWF0b3I+CiAgICAgIDxjcmVhdG9yTmFtZT5CaXdlbiBHYW88L2NyZWF0b3JOYW1lPgogICAgICA8YWZmaWxpYXRpb24+Qm9zdG9uIFVuaXZlcnNpdHk8L2FmZmlsaWF0aW9uPgogICAgPC9jcmVhdG9yPgogICAgPGNyZWF0b3I+CiAgICAgIDxjcmVhdG9yTmFtZT5NZW5nIFpoYW5nPC9jcmVhdG9yTmFtZT4KICAgICAgPGFmZmlsaWF0aW9uPkJvc3RvbiBVbml2ZXJzaXR5PC9hZmZpbGlhdGlvbj4KICAgIDwvY3JlYXRvcj4KICAgIDxjcmVhdG9yPgogICAgICA8Y3JlYXRvck5hbWU+UWluZyBYaWE8L2NyZWF0b3JOYW1lPgogICAgICA8YWZmaWxpYXRpb24+Qm9zdG9uIFVuaXZlcnNpdHk8L2FmZmlsaWF0aW9uPgogICAgPC9jcmVhdG9yPgogICAgPGNyZWF0b3I+CiAgICAgIDxjcmVhdG9yTmFtZT5KaS1YaW4gQ2hlbmc8L2NyZWF0b3JOYW1lPgogICAgICA8YWZmaWxpYXRpb24+Qm9zdG9uIFVuaXZlcnNpdHk8L2FmZmlsaWF0aW9uPgogICAgPC9jcmVhdG9yPgogIDwvY3JlYXRvcnM+CiAgPHRpdGxlcz4KICAgIDx0aXRsZSB4bWw6bGFuZz0iZW4tVVMiPkNoZW0tU0lNOiBTdXBlci1yZXNvbHV0aW9uIENoZW1pY2FsIEltYWdpbmcgdmlhIFBob3RvdGhlcm1hbCBNb2R1bGF0aW9uIG9mIFN0cnVjdHVyZWQtSWxsdW1pbmF0aW9uIEZsdW9yZXNjZW5jZTwvdGl0bGU+CiAgPC90aXRsZXM+CiAgPHB1Ymxpc2hlcj5Db2RlIE9jZWFuPC9wdWJsaXNoZXI+CiAgPHB1YmxpY2F0aW9uWWVhcj4yMDI2PC9wdWJsaWNhdGlvblllYXI+CiAgPHJlc291cmNlVHlwZSByZXNvdXJjZVR5cGVHZW5lcmFsPSJTb2Z0d2FyZSI+Q2Fwc3VsZTwvcmVzb3VyY2VUeXBlPgogIDxzdWJqZWN0cz4KICAgIDxzdWJqZWN0PkNhcHN1bGU8L3N1YmplY3Q+CiAgICA8c3ViamVjdD5CaW9sb2d5PC9zdWJqZWN0PgogIDwvc3ViamVjdHM+CiAgPGNvbnRyaWJ1dG9ycy8+CiAgPGRhdGVzPgogICAgPGRhdGUgZGF0ZVR5cGU9IkFjY2VwdGVkIj4yMDI2LTA1LTE2PC9kYXRlPgogIDwvZGF0ZXM+CiAgPGxhbmd1YWdlPmVuLVVTPC9sYW5ndWFnZT4KICA8YWx0ZXJuYXRlSWRlbnRpZmllcnM+CiAgICA8YWx0ZXJuYXRlSWRlbnRpZmllciBhbHRlcm5hdGVJZGVudGlmaWVyVHlwZT0iQ29kZSBPY2VhbiBJRCI+ZmFlNmY3ZDMtNWI3My00MzcwLTgwNWYtMzg0ZmFiZDcxNTRiPC9hbHRlcm5hdGVJZGVudGlmaWVyPgogICAgPGFsdGVybmF0ZUlkZW50aWZpZXIgYWx0ZXJuYXRlSWRlbnRpZmllclR5cGU9IkNvZGUgT2NlYW4gU2x1ZyI+MTU0NTMyNjwvYWx0ZXJuYXRlSWRlbnRpZmllcj4KICA8L2FsdGVybmF0ZUlkZW50aWZpZXJzPgogIDxyZWxhdGVkSWRlbnRpZmllcnMvPgogIDxzaXplcy8+CiAgPGZvcm1hdHMvPgogIDx2ZXJzaW9uPjIuMDwvdmVyc2lvbj4KICA8cmlnaHRzTGlzdD4KICAgIDxyaWdodHMgcmlnaHRzVVJJPSJodHRwczovL29wZW5zb3VyY2Uub3JnL2xpY2Vuc2VzL01JVCI+TUlUIGxpY2Vuc2U8L3JpZ2h0cz4KICAgIDxyaWdodHMgcmlnaHRzVVJJPSJodHRwczovL2NyZWF0aXZlY29tbW9ucy5vcmcvc2hhcmUteW91ci13b3JrL3B1YmxpYy1kb21haW4vY2MwLyI+Tm8gUmlnaHRzIFJlc2VydmVkIChDQzApPC9yaWdodHM+CiAgPC9yaWdodHNMaXN0PgogIDxkZXNjcmlwdGlvbnM+CiAgICA8ZGVzY3JpcHRpb24gZGVzY3JpcHRpb25UeXBlPSJBYnN0cmFjdCI+VGhlIGNhcHN1bGUgZm9jdXNlcyBvbiB0d28gbW9kdWxlcyB1c2VkIGluIENoZW0tU0lNOgoKKipQLU1MRCAoUG9pc3NvbiBNYXhpbXVtLUxpa2VsaWhvb2QgRGVtb2R1bGF0aW9uKSoqCgpBIHN0YXRpc3RpY2FsbHkgZ3JvdW5kZWQgZGVtb2R1bGF0aW9uIG1ldGhvZCBmb3Igc3RydWN0dXJlZC1pbGx1bWluYXRpb24gcGhvdG90aGVybWFsIG1vZHVsYXRpb24gZGF0YS4gUC1NTEQgbW9kZWxzIHRoZSBwYWlyZWQgSG90L0NvbGQgcGhvdG9uLWNvdW50IG1lYXN1cmVtZW50cyB1bmRlciBhIGZvcndhcmQgU0lNIG1vZHVsYXRpb24gbW9kZWwgYW5kIGVzdGltYXRlcyBtb2R1bGF0aW9uLWFtcGxpdHVkZSBpbWFnZXMgdmlhIFBvaXNzb24gbWF4aW11bS1saWtlbGlob29kIGZpdHRpbmcuIFRoaXMgYXBwcm9hY2ggaXMgZGVzaWduZWQgdG8gaW1wcm92ZSByb2J1c3RuZXNzIGluIHBob3Rvbi1saW1pdGVkIHJlZ2ltZXMgYW5kIHRvIHJlZHVjZSBhcnRpZmFjdHMgdGhhdCBjYW4gYXJpc2UgZnJvbSBjb252ZW50aW9uYWwgZGlmZmVyZW5jaW5nLWJhc2VkIGRlbW9kdWxhdGlvbi4KCioqc3BlY05vcm0gKFNwZWN0cmFsIE5vcm1hbGl6YXRpb24pOioqCgpBIGh5cGVyc3BlY3RyYWwgbm9ybWFsaXphdGlvbiB3b3JrZmxvdyB0aGF0IHN0YWJpbGl6ZXMgQ2hlbS1TSU0gc3BlY3RyYSBhY3Jvc3Mgd2F2ZW51bWJlcnMgYW5kIGhlbHBzIGRlY291cGxlIGNoZW1pY2FsIGNvbnRyYXN0IGZyb20gZmx1b3Jlc2NlbmNlIGJyaWdodG5lc3MgdmFyaWF0aW9ucy4gc3BlY05vcm0gcGVyZm9ybXMgaW50ZW5zaXR5IHJlZmVyZW5jaW5nIGFuZCBzcGVjdHJhbCBzY2FsaW5nIHRvIHlpZWxkIGNvbnNpc3RlbnQsIGNvbXBhcmFibGUgc3BlY3RyYSBhY3Jvc3MgcGl4ZWxzIGFuZCBhY3Jvc3Mgd2F2ZWxlbmd0aHMuPC9kZXNjcmlwdGlvbj4KICA8L2Rlc2NyaXB0aW9ucz4KICA8Z2VvTG9jYXRpb25zLz4KICA8ZnVuZGluZ1JlZmVyZW5jZXMvPgo8L3Jlc291cmNlPg==","url":"https://codeoc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