viewer: incorporate the svg objects ontop of open-seadragon in the viewerapp

[hongsudt]

Background:

• The viewer app replies on the open-seadragon repo. https://github.com/informatics-isi-edu/openseadragon-viewer. You can ask @lperman or @svoinea on how this component is deployed. @jrchudy might be able to help you as well since he briefly worked on the viewer app before.
• The annotation (an area and an anatomical name) is done in the viewer app. There should be some code that allow you to render a rectangle in multi-zoom display.

Test data

• Specimen: Q-296R
• czi file: https://www.gudmap.org/hatrac/resources/histological_images/2017/c8334e8d29b9261493d922fafc81350c?uinit=1&cid=record
• location to pyramid: /var/www/html/openseadragon-viewer/mview.html?url=/data/2017/c8334e8d29b9261493d922fafc81350c
• Sample svgs can be found on https://dev.gudmap.org/data/annotations/poc/Q-296R_all_contours_cw_named.svg on rbk-dev. This svg corresponds to specimen Q-296R.
• XML: https://dev.gudmap.org/data/annotations/poc/Q-296R_20160707-hKDCS19_133-JAM-0-30-000_all-contours.xml

Tasks:

• Assume an svg input (or multiple svg files), make sure we can toggle the display of each annotation object.
• Provide a navigation for users to turn on/off the overlay.
• There should be a way to get from the overlay to the term, and vice versa.

[carlkesselman]

There seem to ba a number of ways to do this. Should consider best approach. Here is one:

https://bl.ocks.org/fabiovalse/71bbbd5c87a148f1c7fabc97b0bbc980

and https://github.com/openseadragon/openseadragon/issues/1425

D3 is probably the most general way of doing this.

Carl

---

Dr. Carl Kesselman Dean’s Professor, Epstein Department of Industrial and Systems Engineering Fellow, Information Sciences Institute Viterbi School of Engineering

Professor, Preventive Medicine Keck School of Medicine

University of Southern California 4676 Admiralty Way, Suite 1001, Marina del Rey, CA 90292-6695 Phone: +1 (310) 448-9338 Email: carl@isi.edumailto:carl@isi.edu Web: http://www.isi.edu/~carl

On May 9, 2019, at 4:17 PM, Hongsuda notifications@github.com<mailto:notifications@github.com> wrote:

Background:

• The viewer app replies on the open-seadragon repo. https://github.com/informatics-isi-edu/openseadragon-viewer. You can ask @lperman or @svoineahttps://github.com/svoinea on how this component is deployed. @jrchudyhttps://github.com/jrchudy might be able to help you as well since he briefly worked on the viewer app before.
• The annotation (an area and an anatomical name) is done in the viewer app. There should be some code that allow you to render a rectangle in multi-zoom display.

Tasks:

• Assume an svg input (or multiple svg files), make sure we can toggle the display of each annotation object.
• Provide a navigation for users to turn on/off the overlay.
• There should be a way to get from the overlay to the term, and vice versa.

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[iamyle0710]

The coordinates used in the XML file doesn't seem to match with the one used in openseadragon. I was able to draw the contours, but unable to locate/resize them without knowing the coordinate system used in the file. It appears that the contours are meant for the third section from just visually matching them with the original image.

• The drawn contours from the XML file

• Third section of the image in openseadragon