Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[Docs] Improved the Adding a Slide section #4

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open

[Docs] Improved the Adding a Slide section #4

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
20 changes: 18 additions & 2 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -78,9 +78,25 @@ If an instance is secured, users of caMicroscope need a user entry in the ‘use

### Adding Slides

For any slide to be visible in caMicroscope, the WSI file must exist, and there must be a record in the database to describe it.
For any slide to be visible in caMicroscope, the Whole Slide Image (WSI) file must exist, and there must be a record in the database to describe it. Both of these can be added simultaneously through the caMicroscope UI.

Both of these can be added simultaneously through the caMicroscope UI. From the table, click upload, pick a compatible file, then give the slide a unique name. The same process works for the batch uploader, which can be found as an extended option of the download button from the table.
Follow these steps to add a slide:
1. Navigate to the slides tab in caMicroscope UI
2. From the table, click upload

![image](https://github.com/camicroscope/docs/assets/122698422/77567b98-773d-4657-a780-91c31ad71592)

3. Choose a compatible file (svs or DICOM). You can upload a file in three ways:
1. From your local folder
2. From your Google drive
3. Using a URL

The file name and token field should fill automatically.
> Note: If the file name is not automatically filled when you upload the file, you will have to fill it in manually. If this occurs, be sure to add the file extension after the file name, like this _sampleslide.svs_
4. Give the slide a unique name, then click the right-pointing arrow.
5. Click the Finish Upload button

The same process works for the batch uploader, which can be found as an extended option of the download button from the table.

If the slides are already present, you can use SlideUtil.py within the ca-load container or pod (for docker, use `docker exec -it ca-load`). This requires a manifest of slides which should already exist in the ./images/ (or customized location) filesystem mount. This is useful if you’re working on a system with existing slide images, where you can remap the ./images mount to any location on the host server.

Expand Down