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DIDSR / eeDAP

Evaluation Environment for Digital and Analog Pathology
http://didsr.github.io/eeDAP/
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Registration between two WSI #83

Closed qigongFDA closed 3 years ago

qigongFDA commented 6 years ago

We will create a new feature to register two WSI images. Then we can share annotation from one image to the other.

qigongFDA commented 6 years ago

Here is a potential GUI interface. image WSIregistration.pptx

brandon-gallas commented 6 years ago

Good idea.

qigongFDA commented 5 years ago

Here is the screen cut of GUI. Capture

qigongFDA commented 5 years ago

I create GUI to do the registration between WSIs. WSI A: Basic WSI. We have positions for this WSI. WSI B: Target WSI. We want position for this WSI.

Procedure:

  1. Load two WSIs
  2. Click "Start Registration" button
  3. Use the 3 buttons and click WSI thumbnail to do registration.
  4. After the registration done, the "Transformation Equation" displayed.
  5. Click "Load WSI A position" button to load WSI A's positions.
  6. Click "Export position for the target WSI" button to generate the positions for target WSI and save to disc.

Format of position file:

  1. CSV.
  2. Two columns, (X and Y)
brandon-gallas commented 5 years ago

Nice. Can you add a feature that allows the user to manually input an x,y position on slide A and return the x,y position on slide B?

Also, work on the documentation and we will find someone to review for feedback. Do the documentation in some simple format that we can ultimately add as a wiki FAQ page.

The priority for documenting is not high. Glad that we now have the tool.

KKIverson commented 4 years ago

Have you finished this new feature: Registration between two WSI?

brandon-gallas commented 4 years ago

Yes. The code is here https://github.com/DIDSR/eeDAP/tree/master/utilities/WSI_to_WSI_registration

The specific script to run is https://github.com/DIDSR/eeDAP/blob/master/utilities/WSI_to_WSI_registration/WSIregistration.m

Instructions are in the comment above LINK and this picture might help too.

image

jiajundeng commented 3 years ago

I create GUI to do the registration between WSIs. WSI A: Basic WSI. We have positions for this WSI. WSI B: Target WSI. We want position for this WSI.

Procedure:

  1. Load two WSIs
  2. Click "Start Registration" button
  3. Use the 3 buttons and click WSI thumbnail to do registration.
  4. After the registration done, the "Transformation Equation" displayed.
  5. Click "Load WSI A position" button to load WSI A's positions.
  6. Click "Export position for the target WSI" button to generate the positions for target WSI and save to disc.

Format of position file:

  1. CSV.
  2. Two columns, (X and Y)

Hi, I would like to ask is it possible that you can offer me the mathematical prove or theoretical support while you do the whole slide image registration? In other words, what is your underlying principle when performing the wsi registration process. What is your reference paper when implementing the wsi registration?

brandon-gallas commented 3 years ago

The registration is described in these papers.