does anybody know that wether the MRI images of each patient’s glioblastoma match spatially with the resected tumor which cut into tissue blocks in Ivy GAP glioblastoma database?that is ,can we be able to find the corresponding partition on the MRI image according to the tissue block of the resected tumor ,as flowing:
Dear Qin,
Welcome to the Community Forum, and thank you for your question.
Mapping biopsy samples collected with stereotactic MRIs will enable precise localization of the biopsy in 3D space using histopathological features extracted from the data. At least one study surveyed each patient’s tumor prior to surgery multiple times with such stereotactic needle biopsies to compare multiple MRI coordinates to their histopathological counterparts.
In the Ivy GAP, accurate mapping of the resected tumor blocks to the MRI in 3D space is limited by a number of factors. Not all patients had Stealth computer navigation assisted surgery, so the spatial designations (A/P, L/M, D/V) in each resected tumor image are approximate. Non-native fiducials were not placed within the tumor for the purposes of mapping to the MRI. The tumor loses its original 3D shape as soon as it is resected. Placement of the resected tumor on a hard surface further distorts its shape. Not all tumor blocks were assessed for every tumor; only the best were used, and highly necrotic blocks were not assessed by ISH and H&E. Not all sub-blocks within each tumor block were assessed by ISH or H&E; some were highly necrotic. Assessment by ISH and H&E of only 5-15% of each good tumor block was needed for construction of the atlas. In spite of these challenges, it might be feasible to map the tumor blocks to MRI features to some extent using the resected tumor images and histopathological features with the help from algorithms that stretch and warp the image data.
Ralph Puchalski
Dear Ralph Puchalski,
Thank you very much, we are very grateful for your answer, best wishes.
your sincerely
Qin
Hi Ralph,
I am wondering what RNAseq data from the IVY GAP have MRI coordinates? I downloaded all of the 10642 Leading edge data and the MRI coordinates listed in spreadsheet were all -1. I would greatly appreciate any related information you could provide!! Thank you!
Dear AustinKunch,
Please see my reply to you under your other inquiry: MRI coordinates of IVY GAP RNAseq data:
The Ivy GAP does not have any data based on region, ISH, tissue block, or LMD-RNA-Seq sample that is tied to MRI coordinates. In other Allen Institute atlases, -1 is typically used to represent coordinates with no data (e.g., locations with no anatomical coordinates). There are other users of the Ivy GAP who have attempted to map the histology data, or at least tissue block, to the MRIs, but I am not sure what the status is of these efforts. As I explained to Qin in this forum’s same topic, accurate mapping probably cannot be achieved without multiple stereotactic biopsy MRIs for each patient, which was not done for the Ivy GAP.
Thank you,
Ralph