Deep learning for digital pathology image analysis: A comprehensive tutorial with selected use cases is a paper introducing and demonstrating the use Machine/Deep Learning for Digital Pathology use-cases. It does so by considering 7 use cases.

Types of tasks

The 7 tasks can be divided into 3 kinds of problems.

Project: OpenMRS Atlas 3.1

Primary Mentor: Burke Mamlin

Backup Mentor: Harsha Kumara

Student: Sai Sandeep Mutyala

Project Link:


As OpenMRS infrastructure moved towards using LDAP, the PHP implementation of Atlas started to break. Efforts on converting Atlas to Node were started in a previous year’s GSoC project, where most of the front-end was setup. The objective of the project is to fix the missing pieces in the Node version of Atlas, and also integrate Atlas with the Atlas module. A lot of new features were also implemented as part of this project.



I tweaked a few older PRs, and the atlas module PRs got merged. Burke created amazing mockups for a few tickets, so I reworked their UI a little. The final evaluations begin tomorrow, so that’s something to look forward to.

Major changes this week were:

ATLAS-169: Marker search was implemented for this PR.

Here’s Burke’s mockup,

And here’s the search UI.

This week felt more productive than the last one. Burke created a bunch of new tickets. More github contributions for me! :)

Some notable tickets were:

ATLAS-201: Enabled Google Analytics for Atlas.

ATLAS-202: Improved server logging by expanding on the use of log4js. Switched morgan to run in combined mode.

ATLAS-205: The modules used by a site will no longer to exposed by the API for security reasons.

ATLAS-206: A reporting API for modules was created to know the popularity and usage of certain modules.

ATLAS-207: A reports page was suggested to see know usage statistics of Atlas. …

Work on the Atlas module was started this week. I made 2 PRs but they have yet to be reviewed and refined. I was sick and busy with some personal work this week so I couldn’t put in more than 20 hours, but I’ll be making up for it next week.

The task of making the atlas module work with atlas was divided into 2 issues:

ATLAS-194: A ‘module mode’ is created, which allows users to interact differently with Atlas when viewing it through a module. As part of this task, cross-window communication was established between the module page and…

This week, the PR to send mails to owners of fading markers got merged. A bunch of bugs in Atlas got fixed, and the updated Atlas was deployed to production! :D

Thanks to Ellen, we discovered that a lot of usernames in the database were stored as ‘openmrs_id:<username>’ rather than just ‘<username>’. This was quickly fixed and pushed onto production by Burke.

  • ATLAS-168: User’s of fading markers are sent mails which provide them quick links to update/delete their markers.
  • ATLAS-125: The Atlas Module hasn’t been working with the Atlas Server. Work was started to get the 2 to work together.

This week, some important PRs which I opened last week were refined and merged. There are a lot of database related PRs. A few tiny bug fixes were made, and also a PR was made to send mails to owners and co-owners of fading markers, but its still in the making. :)

ATLAS-166: Allow creators to add ‘co-owners’ to markers. Co-owners can edit markers.

ATLAS-178: Support upload of marker image. The PR got merged earlier this week after a few minor bug fixes.

ATLAS-184: Previously, there were several MySQL scripts to create the database. …

An RSS feed was added to Atlas, and a system to allow multiple users to edit markers was created!

Some tickets I worked on, this week are:

  • ATLAS-126: An RSS feed for changes on the Atlas was created and can be accessed using ‘{baselink}/rss’. As part of the ticket, {baselink}/?marker={marker id} can be used to spot individual markers on the Atlas. The RSS feed was created using node-rss.
RSS Feed

Related tickets: ATLAS-187, ATLAS-188

  • ATLAS-166: The ticket aims to allow multiple users to manage a single marker. Creators of markers can add ‘Co-owners’ to edit/update markers for them. …

This week consisted of a major improvement in the way the Atlas API functions, a few bug fixes, and a few nice new features. :)

Here are the tickets solved this week:

(The links to the respective PRs are in the comments section of JIRA)

ATLAS-175: The POST, PATCH, and DELETE routes of the API previously returned only the id, or nothing. Now, they return the entire resource.

ATLAS-181: Clicking on alerts’ backdrop dismisses the alert.

ATLAS-174: Clustering feature for markers was fixed.

ATLAS-176: As the number of markers on Atlas increases, spotting one’s own markers becomes more and more…

Week 5 has come to an end and we’re getting closer to the deployment of Atlas 3.x to production. This week consisted of mostly bug fixes, and a lot of tickets were solved. Burke was extremely responsive this week and PRs got merged daily, really speeding up the process. Atlas 3.x was merged into master by Cintia yesterday. I also got contributor rights on the repo, so that’s nice. :)

Since the Rest API for types/versions/distributions got merged (ATLAS-145), testing the admin pages became possible. …

Sai Sandeep Mutyala

Get the Medium app

A button that says 'Download on the App Store', and if clicked it will lead you to the iOS App store
A button that says 'Get it on, Google Play', and if clicked it will lead you to the Google Play store