https://informatics-analytics.dfci.harvard.edu/ en https://informatics-analytics.dfci.harvard.edu/pathml-tools-computational-pathology <span class="field field--name-title field--type-string field--label-hidden">PathML tools for computational pathology</span> <div class="field field--name-field-institutions field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/2" hreflang="en">DF/HCC</a></div> <div class="field__item"><a href="/taxonomy/term/1" hreflang="en">DFCI</a></div> <div class="field__item"><a href="/taxonomy/term/3" hreflang="en">Outside participating sites</a></div> </div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/user/155" typeof="schema:Person" property="schema:name" datatype="">biodata</span></span> <span class="field field--name-created field--type-created field--label-hidden">Sat, 06/01/2024 - 19:32</span> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p><strong>PathML objective is to lower the barrier to entry to digital pathology.</strong></p> <p>Examples:</p> <ol dir="auto"> <li><a href="https://github.com/Dana-Farber-AIOS/pathml/blob/master/examples/loading_images_vignette.ipynb">Load over 160+ different types of pathology images using PathML</a></li> <li><a href="https://github.com/Dana-Farber-AIOS/pathml/blob/master/examples/stain_normalization.ipynb">H&amp;E Stain Deconvolution and Color Normalization</a></li> <li><a href="https://github.com/Dana-Farber-AIOS/pathml/blob/master/examples/workflow_HE_vignette.ipynb">Brightfield imaging pipeline: load an image, preprocess it on a local cluster, and get it read for machine learning analyses in PyTorch</a></li> <li><a href="https://github.com/Dana-Farber-AIOS/pathml/blob/master/examples/multiplex_if.ipynb">Multiparametric Imaging: Quickstart &amp; single-cell quantification</a></li> <li><a href="https://github.com/Dana-Farber-AIOS/pathml/blob/master/examples/codex.ipynb">Multiparametric Imaging: CODEX &amp; nuclei quantization</a></li> <li><a href="https://github.com/Dana-Farber-AIOS/pathml/blob/master/examples/train_hovernet.ipynb">Train HoVer-Net model to perform nucleus detection and classification, using data from PanNuke dataset</a></li> <li><a href="https://github.com/Dana-Farber-AIOS/pathml/blob/master/examples/pathml_gallery.ipynb">Gallery of PathML preprocessing and transformations</a></li> </ol> <p>More information at: <a href="https://github.com/Dana-Farber-AIOS/pathml" rel=" noopener" target="_blank">https://github.com/Dana-Farber-AIOS/pathml</a></p> <p>in a hurry? &nbsp;&nbsp;<em>docker pull pathml/pathml &amp;&amp; docker run -it -p 8888:8888 pathml/pathml</em></p> </div> <div class="field field--name-field-users field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/30" hreflang="en">Analytics users</a></div> <div class="field__item"><a href="/taxonomy/term/20" hreflang="en">Basic researchers</a></div> <div class="field__item"><a href="/taxonomy/term/11" hreflang="en">Clinical researchers</a></div> </div> <div class="field field--name-field-access-and-support-url-or- field--type-link field--label-hidden field__item"><a href="https://www.pathml.org">PathML website</a></div> <div class="field field--name-field-fast-find-service-link field--type-entity-reference field--label-hidden field__item"><a href="/taxonomy/term/8" hreflang="en">Technical Support</a></div> Sat, 01 Jun 2024 23:32:50 +0000 biodata 202 at https://informatics-analytics.dfci.harvard.edu https://informatics-analytics.dfci.harvard.edu/redcap-0 <span class="field field--name-title field--type-string field--label-hidden">REDCap</span> <div class="field field--name-field-institutions field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/2" hreflang="en">DF/HCC</a></div> <div class="field__item"><a href="/taxonomy/term/1" hreflang="en">DFCI</a></div> </div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/user/159" typeof="schema:Person" property="schema:name" datatype="">rio</span></span> <span class="field field--name-created field--type-created field--label-hidden">Mon, 03/04/2024 - 15:18</span> <div class="clearfix text-formatted field field--name-field-brief-description field--type-text field--label-hidden field__item">REDCap provides a secure web application for building and managing online surveys and databases.</div> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p><strong>REDCap</strong>&nbsp;(<strong>R</strong>esearch&nbsp;<strong>E</strong>lectronic&nbsp;<strong>D</strong>ata&nbsp;<strong>Cap</strong>ture) is a secure, HIPAA-compliant web-based application designed for data collection for&nbsp;research studies. It enables rapid project development and provides users with advanced functionality, complete autonomy and control of projects, and direct exports to common statistical packages.</p> <p>COMING:&nbsp;</p> <ul> <li>REDCap eConsent Part-11 Compliant System</li> </ul> </div> <div class="field field--name-field-users field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/20" hreflang="en">Basic researchers</a></div> <div class="field__item"><a href="/taxonomy/term/11" hreflang="en">Clinical researchers</a></div> <div class="field__item"><a href="/taxonomy/term/13" hreflang="en">Clinical trial administration</a></div> <div class="field__item"><a href="/taxonomy/term/16" hreflang="en">Research administrators</a></div> <div class="field__item"><a href="/taxonomy/term/12" hreflang="en">Research staff</a></div> </div> <div class="field field--name-field-access-and-support-url-or- field--type-link field--label-hidden field__item"><a href="https://wiki.dfci.harvard.edu:8443/rdc2">DFCI REDCap User Documentation</a></div> <div class="field field--name-field-fast-find-service-link field--type-entity-reference field--label-hidden field__item"><a href="/taxonomy/term/5" hreflang="en">Clinical Research and Research Administration Software</a></div> Mon, 04 Mar 2024 20:18:49 +0000 rio 197 at https://informatics-analytics.dfci.harvard.edu https://informatics-analytics.dfci.harvard.edu/websites-research-and-clinical-programs <span class="field field--name-title field--type-string field--label-hidden">Websites for research and clinical programs</span> <div class="field field--name-field-institutions field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/2" hreflang="en">DF/HCC</a></div> <div class="field__item"><a href="/taxonomy/term/1" hreflang="en">DFCI</a></div> <div class="field__item"><a href="/taxonomy/term/3" hreflang="en">Outside participating sites</a></div> </div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/user/1" typeof="schema:Person" property="schema:name" datatype="">admin</span></span> <span class="field field--name-created field--type-created field--label-hidden">Mon, 12/07/2020 - 14:11</span> <div class="clearfix text-formatted field field--name-field-brief-description field--type-text field--label-hidden field__item">Graphic design, content, programming, social media, and hosting </div> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>DFCI’s <a href="http://www.healthcommcore.org" rel="noopener noreferrer" target="_blank">Health Communication Core</a> develops websites ranging from simple, static sites to complex, interactive web applications. The HCC creative team provides professional writing, graphic design, programming, social media, and strategy development services for:</p> <ul> <li>Research recruitment/retention</li> <li>Online interventions</li> <li>Decision aid development</li> <li>Research dissemination</li> <li>Awareness and outreach</li> </ul> <p>Contact <a href="mailto:health_communication@dfci.harvard.edu" rel="noopener noreferrer" target="_blank">health_communication@dfci.harvard.edu</a> to explore how HCC can help strengthen your online presence.</p> </div> <div class="field field--name-field-users field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/20" hreflang="en">Basic researchers</a></div> <div class="field__item"><a href="/taxonomy/term/11" hreflang="en">Clinical researchers</a></div> </div> <div class="field field--name-field-fast-find-service-link field--type-entity-reference field--label-hidden field__item"><a href="/taxonomy/term/4" hreflang="en">Basic Research Software</a></div> Mon, 07 Dec 2020 19:11:39 +0000 admin 131 at https://informatics-analytics.dfci.harvard.edu https://informatics-analytics.dfci.harvard.edu/oncpro <span class="field field--name-title field--type-string field--label-hidden">OncPro</span> <div class="field field--name-field-institutions field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/2" hreflang="en">DF/HCC</a></div> </div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/user/7" typeof="schema:Person" property="schema:name" datatype="">KRT9</span></span> <span class="field field--name-created field--type-created field--label-hidden">Fri, 07/19/2019 - 14:14</span> <div class="clearfix text-formatted field field--name-field-brief-description field--type-text field--label-hidden field__item">Oncology Protocol system storing current IRB-approved study documents (e.g. protocol, consent, etc.)</div> <div class="field field--name-field-users field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/11" hreflang="en">Clinical researchers</a></div> <div class="field__item"><a href="/taxonomy/term/13" hreflang="en">Clinical trial administration</a></div> <div class="field__item"><a href="/taxonomy/term/12" hreflang="en">Research staff</a></div> </div> <div class="field field--name-field-access-and-support-url-or- field--type-link field--label-hidden field__item"><a href="https://www.dfhcc.harvard.edu/crs-resources/ODQ_Documents/07_Education/DFHCC_New_Researcher_Checklist.docx">DF/HCC New Researcher Checklist</a></div> Fri, 19 Jul 2019 18:14:24 +0000 KRT9 18 at https://informatics-analytics.dfci.harvard.edu https://informatics-analytics.dfci.harvard.edu/oncdrs <span class="field field--name-title field--type-string field--label-hidden">OncDRS</span> <div class="field field--name-field-institutions field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/2" hreflang="en">DF/HCC</a></div> </div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/user/1" typeof="schema:Person" property="schema:name" datatype="">admin</span></span> <span class="field field--name-created field--type-created field--label-hidden">Mon, 06/24/2019 - 14:32</span> <div class="clearfix text-formatted field field--name-field-brief-description field--type-text field--label-hidden field__item">Oncology Data Retrieval System</div> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>Data retrieval tool enabling researchers and/or investigators to obtain clinical, genomic, and specimen oncology data for research, including feasibility through publication. To initiate a new data request, please fill out a <a href="https://partnershealthcare.service-now.com/isservicehub?id=sc_cat_item&amp;sys_id=c98acc6b1bb220909f83986cbc4bcbf8" rel=" noopener" target="_blank">DFCI Research Data Services Request Form</a> via ServiceNow to be connected with an OncDRS Navigator</p> </div> <div class="field field--name-field-users field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/20" hreflang="en">Basic researchers</a></div> <div class="field__item"><a href="/taxonomy/term/11" hreflang="en">Clinical researchers</a></div> <div class="field__item"><a href="/taxonomy/term/12" hreflang="en">Research staff</a></div> </div> <div class="field field--name-field-access-and-support-common- field--type-entity-reference field--label-hidden field__item"><a href="/taxonomy/term/19" hreflang="en">IS Service Hub instructions</a></div> Mon, 24 Jun 2019 18:32:44 +0000 admin 12 at https://informatics-analytics.dfci.harvard.edu https://informatics-analytics.dfci.harvard.edu/inform <span class="field field--name-title field--type-string field--label-hidden">InForm</span> <div class="field field--name-field-institutions field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/2" hreflang="en">DF/HCC</a></div> <div class="field__item"><a href="/taxonomy/term/3" hreflang="en">Outside participating sites</a></div> </div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/user/1" typeof="schema:Person" property="schema:name" datatype="">admin</span></span> <span class="field field--name-created field--type-created field--label-hidden">Mon, 06/17/2019 - 12:38</span> <div class="clearfix text-formatted field field--name-field-brief-description field--type-text field--label-hidden field__item">Electronic data capture and tracking: Manage, clean, store, and retrieve clinical trials data; create electronic case report forms</div> <div class="field field--name-field-users field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/11" hreflang="en">Clinical researchers</a></div> <div class="field__item"><a href="/taxonomy/term/12" hreflang="en">Research staff</a></div> </div> <div class="field field--name-field-access-and-support-url-or- field--type-link field--label-hidden field__item"><a href="https://wiki.dfci.harvard.edu:8443/inform">InForm User Documentation</a></div> Mon, 17 Jun 2019 16:38:04 +0000 admin 3 at https://informatics-analytics.dfci.harvard.edu https://informatics-analytics.dfci.harvard.edu/iris-prms <span class="field field--name-title field--type-string field--label-hidden">iRIS (PRMS)</span> <div class="field field--name-field-institutions field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/2" hreflang="en">DF/HCC</a></div> </div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/user/1" typeof="schema:Person" property="schema:name" datatype="">admin</span></span> <span class="field field--name-created field--type-created field--label-hidden">Mon, 06/17/2019 - 12:37</span> <div class="clearfix text-formatted field field--name-field-brief-description field--type-text field--label-hidden field__item">Protocol Review and Monitoring System (PRMS)</div> <div class="field field--name-field-users field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/11" hreflang="en">Clinical researchers</a></div> <div class="field__item"><a href="/taxonomy/term/13" hreflang="en">Clinical trial administration</a></div> <div class="field__item"><a href="/taxonomy/term/12" hreflang="en">Research staff</a></div> </div> <div class="field field--name-field-access-and-support-url-or- field--type-link field--label-hidden field__item"><a href="https://wiki.dfci.harvard.edu:8443/prms">iRIS Wiki</a></div> Mon, 17 Jun 2019 16:37:27 +0000 admin 2 at https://informatics-analytics.dfci.harvard.edu https://informatics-analytics.dfci.harvard.edu/oncore <span class="field field--name-title field--type-string field--label-hidden">OnCore</span> <div class="field field--name-field-institutions field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/2" hreflang="en">DF/HCC</a></div> </div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span lang="" about="/user/1" typeof="schema:Person" property="schema:name" datatype="">admin</span></span> <span class="field field--name-created field--type-created field--label-hidden">Mon, 06/17/2019 - 12:30</span> <div class="clearfix text-formatted field field--name-field-brief-description field--type-text field--label-hidden field__item">Clinical trial management system: Create reports, track enrollment, initiate billing</div> <div class="field field--name-field-users field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/taxonomy/term/14" hreflang="en">Budget office</a></div> <div class="field__item"><a href="/taxonomy/term/11" hreflang="en">Clinical researchers</a></div> <div class="field__item"><a href="/taxonomy/term/13" hreflang="en">Clinical trial administration</a></div> <div class="field__item"><a href="/taxonomy/term/12" hreflang="en">Research staff</a></div> </div> <div class="field field--name-field-access-and-support-url-or- field--type-link field--label-hidden field__item"><a href="https://wiki.dfci.harvard.edu:8443/oncore">OnCore Wiki</a></div> Mon, 17 Jun 2019 16:30:39 +0000 admin 1 at https://informatics-analytics.dfci.harvard.edu