Ecli

ecli is a portable command line client to access the Keen Eye digital pathonolgy platform. Its primary use is to ease image upload to the platform and get slide information in a convenient way.

This Go implementation is currently a work in progress.

See it In Action

Please have a quick look at this 2 minutes video showing some useful commands to upload a slide to the Keen Eye platform:

Download

Using ecli is easy since it comes as a static binary with no dependencies. Just grab the latest compiled version for your system (or compile from source, see below).

Usage

Just type ecli in a terminal to get a list of available commands.

Ecli is a command line client for the Keen Eye API. Its primary use is to
perform slide upload and get slide information in a convenient way.

Usage:
  ecli [command]

Available Commands:
  applications List all registered applications
  find         Find slides or groups by criteria
  group        Manage groups
  imageformats List all supported image formats
  label        Manage labels
  login        Open a session
  logout       Close current session
  slide        Manage slides
  version      Show tool version

Flags:
      --config string   Config file (default is $HOME/.ecli.json)
  -q, --quiet           Quiet mode, no verbose output
  -t, --toggle          Help message for toggle

Use "ecli [command] --help" for more information about a command.

Tip: for every available commands, you can always get some help and examples by running ecli [command] -h.

Quick Tour

Creating a Config File

ecli needs a config file to run. It holds profile information about the credentials to be used in order to connect and use the Keen Eye API.

By default, ecli will look for an .ecli.json file in the current user's home directory but you may want to specify a different file by using the --config flag.

The config file contains profile information in a JSON file like

{
  "profile1": {
    "login": "<YOUR LOGIN EMAIL ADDRESS>",
    "password": "<YOUR PASSWORD>",
    "url": "https://<YOUR URL TO PLAFORM>/api/v2"
  }
}

with <YOUR URL TO PLAFORM> being the address used by your browser to connect to the platform, like https://prefix.keeneyetechnologies.com. Note that the url defined in the config file must end with /api/v2.

Sessions

Before you can start using the API with ecli, you need to open a session. Log in to the service with ecli login:

$ ecli login profile1
profile1: you have been logged in successfully.

Now you can start using the API with ecli.

Your session may expire 30 minutes later due to inactivity. In this case, you will have to login again. You can also explicitely log out from the service:

$ ecli logout
Your session is now closed.

Labels

Labels provide an easy way to categorize the images and groups based on descriptive titles. They can have a color and a description.

Any number of labels can be applied to images and groups.

Type ecli label -h to see availabe subcommands and examples.

Groups

Groups are like directories in a filesystem, useful to organize images. They can have a name and a description. Labels can be added to groups.

Type ecli group -h to see availabe subcommands and examples.

Image Formats

Use the imageformats command to list all supported image formats for your installation. The first column is the image format value to pass to the slide upload command during an image upload (see section below).

$ ecli imageformats
tiff                           tiff                           TIFF image
ndpi                           ndpi                           NDPI image
ndpis                          ndpis                          NDPIS image
dicom                          dicom                          DICOM image

This is the result from a default installation.

Slide Upload

ecli slide upload can take many parameters, like image format, pixel size (value and unit) and so on. Please type ecli slide upload -h to get the full list of available options.

For example, uploading a TIFF image with a 1 micron pixel size and apply two "retina" and "core" labels on it can be performed with

$ ecli slide upload stained_cells.tif -f tiff -p 1 -l "retina" -l "core"

By default, the slide will be uploaded to the root of the work list. When uploading a slide inside a group somewhere else in the hierarchy is required, the --group-id flag can be used.

Say you need to upload a slide into the existing Study 1 group. You first need to get the group unique ID to use during the upload:

$ ecli group ls
58a173aee779892825712398 "Other Group"                
58a43cc5e779890c2486ca6d "Study 1"

Group Study 1 has ID 58a43cc5e779890c2486ca6d, so to upload the slide into that group, just

$ ecli slide upload stained_cells.tif --group-id 58a43cc5e779890c2486ca6d

Compile From Source

First ensure you have a Go 1.5+ working installation then install the traditional way:

$ go get github.com/keeneyetech/ecli

License

This is free software, see LICENSE.