Getting Started with Codex¶
This Quickstart topic covers some basic tasks and concepts when first logging into Codex.
When you first access a Codex site, you see the home page. You can view information on this specific instance by scrolling down the page, which displays content including how Codex works, facts and figures, social links, and buttons with calls to action. To get started, register an account.
Registering a new account¶
- From the home page, click the Login button in the top right corner.
- Click the Request an invitation link.
- You will be routed to the Request an invitation page.
- Provide the Email address you want to be associated with your account and Your name so the site administrators know who is making the request. Optionally, you can also provide a note to the administrators explaining why you want access, by typing in the Message for administrators field.
- Click the SEND REQUEST button.
- You will receive an email with your temporary login information. Follow the instructions in the email to finish the registration process for your Codex account.
Logging into your account¶
- Click the Login button at the top right of the page.
- Provide your Email address and Password in the fields.
- Toggle the Keep me logged in button to keep yourself logged in for your next session.
- Click the LOGIN button.
Change Your Password¶
To reset the password for your Codex account:
- On the Account Login page, click the Forgot? link below the LOGIN button.
- On the next page, provide the email address associated with your Codex account in the Email address field.
- Click the Reset Password button.
- Check your email inbox where you will receive an account password reset email. If you do not receive this, click the Resend Email button on the Password reset page.
- Click on the link in the email you receive, which will direct you back to the Codex website to create a new password.
- Type in your desired new password and repeat the same password in the Confirm password field. We recommend using at least 8 characters and a combination of letters, numbers, and special characters.
- Click the RESET PASSWORD button. Once you see a confirmation popup message that says you have successfully reset your password, click the Return to login page link.
- Log in with your email address and your newly updated password.
Read Up on Basic Wildbook Concepts¶
Submit and Match Your First Encounters¶
To report a sighting, click the Plus icon in the top right menu bar. You may optionally upload any images, and then indicate how many animals were observed in your sighting. Then you will provide greater detail about the encounter. You are required to indicate the time of the sighting (which could be as specific as the date and time, or as broad as the year), the detection model you’d like to run, and the region in which the sighting occurred. More specific detail may be added as desired. Click “Report Sighting” once you have finished to begin the identification pipeline.
If you uploaded any images, you will be prompted to assign annotations after the animal detection step finishes. For each animal detected, click the Plus icon in its “Annotations” box and then select the image containing a bounding box around the animal you would like associated. You may also add any additional metadata to the animals in the sighting at this point. Press the “Commit” button at the top of the page once you are finished. You then have the option of running an identification job on the image(s) to look for any matches with animals in other sightings.
If you choose to run the identification job, once it has completed you may click “View Match Results” to review potential matches for the animals in your sighting. By default, the match candidates will be ranked according to their system-calculated “score,” or their level of similarity to a given animal in your sighting. If a candidate is a true match, click on “Confirm Match.” You will then either create a new individual (if neither animal is assigned), designate an unassigned animal to an existing individual (if only one is assigned), or merge two individuals (if both are assigned). Once you have finished reviewing matches, you may opt to “Mark sighting reviewed” in the “Actions” dropdown at the top right.
If you forego the identification job, you may still manually identify the animals in your sighting using the “Identify” dropdown in the “Animals” tab to either “Create new individual” or “Manually assign” to an existing individual.
Extend Collaboration Invites¶
Request Further Configuration¶
Bulk Import Legacy Data for Matching¶
The bulk import process allows you to upload images and the associated ecological metadata.
How to Upload Images¶
- From your Codex homepage, click the Actions button in the upper right corner of the screen.
- Select Bulk import. You can only upload images in
- You will be directed to a page where you can upload images. You have the option to either Drop files or Browse files.
- If you have another window open with the photos you want to upload; you can drag them directly to the Bulk import page to upload them.
- You can also select Browse files to locate and upload the images from your device.
- There will be a progress bar at the bottom of the screen showing the progress of your upload. Once everything is uploaded successfully, you will see Complete in place of the progress bar.
- Add more photos by clicking Add more on the upper right corner of the page.
- Select CONTINUE.
How to Upload Metadata¶
- Select UPLOAD SPREADSHEET to upload a
- Once your
.csvfile is uploaded; you will be directed to a page to verify your uploaded data.
- Make sure that the correct rows for column headers are selected.
- After verifying all the data on the
.csvfile, select Confirm mapping or Ignore this column based on your preference.
- Select Review.
- You will be directed to another page to review your data.
- Note that if there are errors, you won’t be able to continue.
- After resolving any errors, select Continue.
- A pop-up window will appear asking you to verify you’re ready to submit your sighting.
- Select Yes to finish bulk importing your information and images.