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Questions about masked tissue and MSI status in PAIP2020 WSI's #3

Open fgfmds opened 4 years ago

fgfmds commented 4 years ago

Can you please explain what the masked tissue represents from a medical perspective in MSI-H and and MSI-L/MSI-S slides respectively? I will explain.

While reviewing the 47 training slides, I noticed a few things which I would like to share.

  1. Slide 4: this image has what looks like a fairly large amount of tissue, and is classified as "0" (low or stable). The masked regions in this slide represent a very small portion of the whole image. Does the masked portion ALWAYS indicate the presence of the MSI anomaly (for both classes)? Can we also infer that the non-masked tissue is ALWAYS normal? Please see slide 4 and corresponding masked image below for reference.

training_data_04_level2_0_sm

training_data_04_level2_0_seg_sm

  1. Slide 6: This image has one masked region which appears to contain a large portion of the whole slide, including mostly tissue but also what looks like areas with no tissue (very light in color; looks like tissue is completely absent). What can you tell me about the light (or completely white areas) which are contained within the mask? Can you also please explain why such areas are included in the mask? This image is classified as "1" so I feel it is important to fully understand how the pathologists determine the exact shape of the contour shown in the mask image. Please see slide 6 and corresponding masked image below for reference.

training_data_06_level2_1_sm

training_data_06_level2_1_seg_sm

Thank you for the opportunity to participate in the competition and I look forward to hearing from you soon!

Paip-2020 commented 4 years ago

Dear @fgfmds

Thank you for inquiry.

A1. Non-masked regions (=normal tissue) → no MSI Masked regions could include the MSI or not, however, non-masked regions are all normal tissues. Thus, no MSI information are in the non-masked regions. Please note that the segmentation of masked regions were drawn by pathologists.

A2. Blank area = empty space = background Based on weak supervision, our task has been set to be more challenging than last year. Thus, the blank area has not been removed. Participants have to deal with it if necessary and you can refer the criteria of blank area(background) in last challenge PAIP2019 here.

fgfmds commented 4 years ago

Thank you for your reply. A couple of follow-up questions if I may:

  1. In the first comment, you mentioned that "masked regions could include MSI or not". If non-MSI tissue is included in a masked region, does that mean that non-MSI tissue is normal? If not, what type of tissue is it?

  2. I am not sure I understand what you mean by "Based on weak supervision" in your second comment. Can you please elaborate?

  3. In your second answer, you stated that "participants have to deal with it (blank area) if necessary". It is not clear to me what the expectation of the organizers is. In other words, Do you expect the predicted mask to NOT have any background included in it?

Thank you again.

Paip-2020 commented 4 years ago

Hi @fgfmds, Q1: In the first comment, you mentioned that "masked regions could include MSI or not". If non-MSI tissue is included in a masked region, does that mean that non-MSI tissue is normal? If not, what type of tissue is it? A1: Please find the dataset description in the PAIP2020 webpage. The masked region means tumor area, so no MSI in the masked region indicates MSS(MSI-stable).

Q2: I am not sure I understand what you mean by "Based on weak supervision" in your second comment. Can you please elaborate? In your second answer, you stated that "participants have to deal with it (blank area) if necessary". It is not clear to me what the expectation of the organizers is. In other words, Do you expect the predicted mask to NOT have any background included in it? A2: Yes, the PAIP hopefully expects the predicted mask does not contain as much background as possible.