camicroscope/slideloader repository overview

⁠SlideLoader

Tool for loading slides and getting slide metadata using openslide

⁠Usage

⁠Upload

Uploading is done in chunks due to the generally large size of the files involved. To upload a slide, you must begin, continue, and finish the upload, as noted in the subsections below.

⁠Begin

Calling a post to the begin route (http://<service url base>/upload/start) will generate a token and a corresponding empty file in the uploading directory. This token is then used for the continue and finish steps.

Note that a file in the uploading directory can be modified by anyone with the token.

⁠Continue

Post filedata encoded in base64 as "data" and the offset as "offset" in a json document in the body to the continue route for the token given (http://<service url base>/upload/continue/<\token>). The data is then written to the temporary file in the uploading directory starting at the given offset, in bytes.

⁠Finish

To prevent further modification to the file, call the finish route (http://<service url base>/upload/finish/<\token>) with the destination filename as "filename" in a json document in the body. In most cases where this fails (such as a rejection for a filename being taken), the temporary file is unchanged so a user can simply try again.

⁠Multiple Image Upload

Place your images into a directory on your filesystem. Then use upload.sh to upload the file. Pass your file path as a parameter. Example: ./upload.sh /path/to/svs/files

⁠Get a Single Image's Metadata

See, for example, http://<service url base>/data/one/<slide filename>

This returns the openslide metadata for the given slide.

⁠Get metadata for a list of image

See, for example http://<service url base>/data/many/["<slide1_filename>", "<slide2_filename>"]

This returns the metadata for each slide.

⁠Loading to caMicroscope

This tool does not communicate with bindaas/drupal/whatever backend is used for slide metadata. Since these data backends have their own method for posting slide metadata, that should be used. This tool can be used as a service oriented way to get slide metadata to then post to the data backend.