[skip ci] DOC: DFBR Jupyter Notebook

[ruqayya]

Notebook to show how to perform WSI registration using the DFBR method, followed by the BSpline approach.

Readthedocs link: https://tia-toolbox.readthedocs.io/en/dfbr_notebook/_notebooks/jnb/10-wsi_registration.html

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[shaneahmed]

Please rename the notebook to 10-wsi-registration.ipynb to make it consistent with current format. We will update it later when we restructure the examples.

[shaneahmed]

Please also upload with results as in other example notebooks.

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Codecov Report

Merging #485 (2fa22a9) into develop (00b6e9c) will increase coverage by 0.00%. The diff coverage is n/a.

@@           Coverage Diff            @@
##           develop     #485   +/-   ##
========================================
  Coverage    99.65%   99.65%           
========================================
  Files           61       61           
  Lines         6044     6064   +20     
  Branches       990      995    +5     
========================================
+ Hits          6023     6043   +20     
  Misses           9        9           
  Partials        12       12           

Impacted Files	Coverage Δ
tiatoolbox/wsicore/wsireader.py	98.06% <0.00%> (+0.05%)	:arrow_up:

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[John-P]

I've just added one comment on NBReview. There is a cell that looks like it should be a heading to me.

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shaneahmed commented on 2022-10-12T09:29:22Z ----------------------------------------------------------------

Please add these two lines

mpl.rcParams["figure.dpi"] = 300  # for high resolution figure in notebook
mpl.rcParams["figure.facecolor"] = "white"  # To make sure text is visible in dark mode

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shaneahmed commented on 2022-10-13T09:22:19Z ----------------------------------------------------------------

This cell needs to be removed from documentation as well.

ruqayya commented on 2022-10-16T21:12:44Z ----------------------------------------------------------------

Done.

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shaneahmed commented on 2022-10-13T09:23:32Z ----------------------------------------------------------------

Do you need to print the transformation matrix?

ruqayya commented on 2022-10-16T21:06:20Z ----------------------------------------------------------------

Removed it.

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shaneahmed commented on 2022-10-13T09:23:33Z ----------------------------------------------------------------

output of this cell can be hidden

ruqayya commented on 2022-10-16T21:08:03Z ----------------------------------------------------------------

You mean hide it from documentation?

shaneahmed commented on 2022-10-16T22:50:37Z ----------------------------------------------------------------

yes

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shaneahmed commented on 2022-10-13T11:38:44Z ----------------------------------------------------------------

Line #2.    !pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git | tail --line 1

Please use @develop

!pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@develop | tail --line 1

shaneahmed commented on 2022-10-18T12:54:24Z ----------------------------------------------------------------

pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@dev-non-rigid-registeration

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shaneahmed commented on 2022-10-13T11:39:29Z ----------------------------------------------------------------

Line #16.    mpl.rcParams["figure.dpi"] = 160  # for high resolution figure in notebook

why not 300?

[shaneahmed]

Please can you also update https://github.com/TissueImageAnalytics/tiatoolbox/blob/develop/examples/README.md

[ruqayya]

Removed it.

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[ruqayya]

You mean hide it from documentation?

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[ruqayya]

Done.

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[shaneahmed]

yes

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[ruqayya]

Please can you also update https://github.com/TissueImageAnalytics/tiatoolbox/blob/develop/examples/README.md

Added here: https://github.com/TissueImageAnalytics/tiatoolbox/blob/DFBR_notebook/examples/README.md#10--image-alignment-10-wsi_registration

[shaneahmed]

pip install git+https://github.com/TissueImageAnalytics/tiatoolbox.git@dev-non-rigid-registeration

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shaneahmed commented on 2022-10-18T12:59:25Z ----------------------------------------------------------------

delete

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shaneahmed commented on 2022-10-18T12:59:26Z ----------------------------------------------------------------

delete

[shaneahmed]

@ruqayya I am merging this PR to create a link on master and to make a release. I will reopen this PR so you can address comments from David.

[shaneahmed]

@ruqayya Please can you create a new PR using the same branch? Please address David's comments in that PR https://github.com/TissueImageAnalytics/tiatoolbox/files/9830884/comments.docx

[ruqayya]

@DavidBAEpstein Thanks for your comments.