GSoC - Coding Period Week 3 | Awesome Hugo blog

Work Done This Week (June 21st to June 27th)

Converted the upgraded segmentation model into ONNX format.
Ran inference on the ONNX model (colab and local environment) to make sure it works. Then used Gradio to build a GUI.
The next step was to host this online. Gradio has their own hosting service, but that costs $7/month. Looked into ways of hosting apps online for free, decided to go with Heroku.
Created the additional files required for hosting online on Heroku:
- Procfile
- requirements.txt
- setup.sh
Pushed the files into a github repository, and linked it to the Heroku app.
Deployed a bare-bones version of the app online.
Adding the centroid mapping feature turned out to be tricky. It worked on local-host, but did not work when deployed on Heroku.
Checked the logs, the error message read :

ImportError: libSM.so.6: cannot open shared object file: No such file or directory
Turns out, it was in issue with OpenCV’s dependency on libSM6. I replaced opencv-python==4.5.2.54 with opencv-python-headless==4.5.2.54 and it worked!
Not everybody has images of C. elegans embryos saved on their computer, so I decided to add in some examples on the site.
Note: The Heroku app is currently linked to a personal repository for quick prototyping and testing.
Links:
- Converting torch model to ONNX - Notebook
- Test repository linked to the cell membrane segmentation heroku app - Link
- Cell membrane segmentation web app (test phase)