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luisvalesilva / wsipre

Handling whole-slide images with region-level annotations.
MIT License
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Annotations in .TIFF format #1

Closed dannellyz closed 4 years ago

dannellyz commented 4 years ago

The dataset I am working on has annotations in TIFF format. Is there a way to incorporate that into this work easily?

luisvalesilva commented 4 years ago

The annotation readers are in the annotation.py module. These are used in the slide.py module here. The two supported annotation styles use the XML format and the arguments are named accordingly.

In order to support a new annotation format, at the very least you'd have to write a dedicated annotation reader and use it in the Slide class.

dannellyz commented 4 years ago

Got it thanks. Do you by chance have a sample of either xml file? The link to the test files seems to be broken.

Appreciate the support!

On Mon, Apr 27, 2020 at 04:41 Luís notifications@github.com wrote:

The annotation readers are in the annotation.py https://github.com/luisvalesilva/wsipre/blob/master/wsipre/annotation.py module. These are used in the slide.py module here https://github.com/luisvalesilva/wsipre/blob/85077ce493253d8512c888908cc203f0c45d1ef1/wsipre/slide.py#L66. The two supported annotation styles use the XML format and the arguments are named accordingly.

In order to support a new annotation format, at the very least you'd have to write a dedicated annotation reader and use it in the Slide class.

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luisvalesilva commented 4 years ago

You can download the two examples used in the demos directly from here (>4 Gb), temporarily.

For context, the two supported annotation types are from two computer vision challenges: CAMELYON16/17 and BACH ICIAR 2018). I haven't checked if the data is still available for download.

Happy to help.

dannellyz commented 4 years ago

Awesome thanks!

On Mon, Apr 27, 2020 at 11:42 Luís notifications@github.com wrote:

You can download the two examples used in the demos directly from here https://drive.google.com/file/d/1j59JJf8126ubVOuig-zBVvgjf7Q_vvM3/view?usp=sharing (>4 Gb), temporarily.

For context, the two supported annotation types are from two computer vision challenges: CAMELYON16/17 https://camelyon17.grand-challenge.org/ and BACH ICIAR 2018 https://iciar2018-challenge.grand-challenge.org/). I haven't checked if the data is still available for download.

Happy to help.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/luisvalesilva/wsipre/issues/1#issuecomment-620066635, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHP5LRIXGIDOGJZYX2X5JHLROWRYHANCNFSM4MRNBLVA .

-- Very Respectfully,

Zac Dannelly LTJG, US Navy

[US] +1 (502) 472-7210 [WhatsApp] +44 (0)7375 322020

"Time is a currency yielding the best returns when invested in others"

luisvalesilva commented 4 years ago

Sure. Good luck with your project! I am closing this.