Myc data set Myc collections from Andrecheck – WSI for mice, in spectrum Ask Ashish if he has retrieved them from box – No markups for WSI Are they needed? – Experimental data / preclinical data Ask Ashish if he has retrieved the data from Spectrum All data fields were filled out in Spectrum – Break down of the pathways  TCGA BrCa dataset – No in-vivo images for mice – Genomic data for mice, expression micro arrays Bob to talk to Eran, data is not at UC Davis at this point – Data for induction and “de-induction” of tumors Before and after images, data is public, data is not at UC Davis at this point

Transplanted mouse cell lines Three model systems – Polyoma Triple negative model – C-neu Her2 positive – Stat1 KO ER, PR positive For all of the above – Expression microarrays UC Davis to verify if the data were put in box and retrieved by Ashish Some data are not public yet, pending publication – WSI (H&E and IHC for ER, PR, Her2, Ki67) At Emory – WSI – quantitative image analysis incl. markup Ashish could not retrieve markups with the images, markups were saved separately, uploaded html files for each of the slides, markups were done in Aperio – Experimental conditions Need to ask Ashish if he downloaded the data from Spectrum; need to take another look at the data – For polyoma and c-Neu in-vivo images (MRI) All images in TCIA – For c-neu MRI and WSI co-registered and annotated Ashish: this is out of scope, need to work on in – Limited sequence data for Stat1 model At UC Davis

Human data Fixation experiment WSI Clinical IHC Mammograms (possibly accessible) microarray

Boone’s CT collection (human, 20 cases) WSI – Spectrum, some are uploaded into Box CT – Uploaded into box – Images do not have DCM headers – Need to figure out if and how to convert – Send box information to Ulli, Ulli to ask David Clunie and/or TCIA for help Clinical information – Some of it is in Spectrum, some in an Excel spreadsheet

Genomic Data Clinical DataPreclinical Data Radiology Images Pathology Images Integrative Query System Data Preclinical

Genomic Data Clinical DataPreclinical Data Radiology Images Pathology Images Integrative Query System Data Tools TCGA TBD

Genomic Data Clinical DataPreclinical Data Radiology Images Pathology Images Integrative Query System Data Tools DB at Emory Spectrum at UC Davis; will go from there to Emory

Genomic Data Clinical DataPreclinical Data Radiology Images Pathology Images Integrative Query System Data Tools Images Markup and Annotations TCIA From UC Davis to TCIA ClinicalPreclinical ePad ClinicalPreclinical

Genomic Data Clinical DataPreclinical Data Radiology Images Pathology Images Integrative Query System Data Tools Images Markup and Annotations TCGA caMicroscope Spectrum caMicroscope ClinicalPreclinical AIM Template Builder AIM Data Service caMicroscope Conversion of Aperio Markups ClinicalPreclinical

Data sets Status Uploading Annotation and markups genomics

Support for pilot challenge Challenge 3 – Preparation of data sets

Genomic DataClinical Data Preclinical Data Radiology Images Pathology Images Integrative Query System TCGA Preclinical TBD ImagesMarkup and Annotations TCI A ??? Spectr um Clini cal Precli nical AIM Template Builder AIM Data Service ePad ClearCanvas Clini cal Precli nical TBD DB TBD TCGA TBD Images Markup and Annotations TCGA Spectrum caMicroscope Clinical Pre- clinical AIM Template Builder AIM Data Service caMicroscope Conversion of Aperio Markups ClinicalPre- clinical

Genomic DataClinical Data Preclinical Data Radiology Images Pathology Images Integrative Query System TCGA Preclinical TBD ImagesMarkup and Annotations TCIA ??? Spectr um Clini cal Precli nical AIM Template Builder AIM Data Service ePad ClearCanvas Clini cal Precli nical TBD DB TBD TCGA TBD Images Markup and Annotations TCGA caMicro Spectrum Clinical Pre- clinical AIM Template Builder AIM Data Service caMicroscope Conversion of Aperio Markups ClinicalPre- clinical Emory WashU UC Davis DICOM WG-30