About bacilleria

Bacillaria is a diatom genus in the Bacillariaceae family.

Cells are elongated and motile, sliding along each other, in stacked colonies. Cells are rectangular in girdle view (when in colonies) and lanceolate in valve view. Raphe system is slightly keeled and runs from pole to pole. Two large plate-like chloroplasts are present, one near each end of the cell. The nucleus is located centrally. Cells are yellow-brown in color. Fibulae are strong, and the valve surface is covered in transverse parallel structures called striae

Types Of bacilleria

• Bacillaria paradoxa.
• Bacillaria paxillifer.

About Project

Our project is mainly focused on implementing a machine learning technique to segment the microscopy images present in our database, and once we have the parameters (feature size, position, directional velocity), we can build a model of Bacillaria motility in conjunction with a member of the DevoWorm group (Dr. Richard Gordon).

Project is divided into different phases.

• Extracting frames from the videos given in the Database.
• Choose segmentation procedure
• Define features within and between frames

  • feature size.

  • feature velocity.

  • directional velocity/time.

Things Completed So far

We have extracted around 18000 frames from the video and uploaded it into the respective drives and GitHub repositories.

Task one is completed.

Things Under Progress

We are currently working to figure out how can segment these images in the best possible way. For this, we have applied many algorithms including watershed, through Sckit-Image, and recently we are working on mask r-CNN procedure. We are currently labeling the the data through manully created mask so that we can train our dataset for further segmentation.

You can find the repo which contains are work here-

https://github.com/devoworm/Digital-Bacillaria/issues/3

That's all for this week 

Thank You.