Purpose

Describe the problem you are trying to solve by packaging your tool as a napari plugin in 1-2 sentences. I should be able to read this alone and communicate the value to someone else.

  • Use Napari to detect the objects in the opened image using the NucleAIzer model.
  • Add the functionality to Napari to train a new nucleAIzer model on your own dataset using transfer learning.

Goals

What would you like to accomplish during the Alfa Cohort collaboration?

  1. Use Napari to detect the objects in the opened image using the NucleAIzer model.
  2. Add the functionality to Napari to train a new nucleAIzer model on your own dataset using transfer learning.

Scope

Key Flows

Show what the end-to-end experience will be for biologists.

[nucleaizer.org workflow, akin to “detect primary objects” in cellprofiler]

A biologist will be able to

  1. Load their own data into napari
  2. Select a nucleAIzer model
  3. Set cell size
  4. Apply the model
  5. View labelled objects
  6. Save or merge with other data for further analysis

[training] A biologist will be able to

  1. Load their own data into napari
  2. Annotate their data
  3. [optional] select an initialization model
  4. Start training
  5. View labelled objects
  6. [optional] Save or share the newly trained model
  7. [upper workflow]

Plan

Milestones

Status: To Do 📝, In Progress 🏗, In Review 🔎, Done ✅

Target Date Milestone Description Status
       
       
2020-04-28 Demo day Demo final plugin 📝