pyGemPick: Flask Web App For Automatic Immunogold Particls Detection

This is the pyGemPick web application built on top of Flask python framework. Here users can download the whole flask web-application or visit the live beta version of the website and process TEM immunogold electron microscopy images quickly, accurately, and free of charge! Have fun detecting those gold particles!!

Setup Redis Server on Mac (osx)

1. Install Homebrew

2. Install Redis Using brew install...

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

brew install redis

####Option A: Launch Redis on Computer Startup

ln -sfv /usr/local/opt/redis/*.plist ~/Library/LaunchAgents

Option B: Launch from Redis-Server Config

redis-server /usr/local/etc/redis.conf

Test if Redis server is running.

redis-cli ping

Response == 'PONG'. (Now Web-app Background Tasks can run!)

Running Virtual Server for Background Tasks

1. Open a separate terminal in the pypick environment. (run source activate pypick)
2. Then run...

rq worker pypick-tasks

Setting up Anaconda Environment

1. Install Anaconda using this tutorial
2. Recreate the environment to run pygempick on Mac/Linux in terminal...
3. To use new environment run source activate pypick command in mac/linux terminal.

Recreating condal env from .yml file

conda env create -n pypick -f pypick_env.yml

Using New Environment

source activate pypick

Setting Up & Updating Database

1. Setup database using flask db init command in terminal.
2. Use flask db migrate command in terminal to update database tables.
3. To push the migration to the live app run flask db upgrade.

Note: Run 2 & 3 every time models.py is modified If this is not done and you accidentally delete a previous migration WITHOUT downgrading, you will have to also delete the logs with it in order to migrate successfully again.

How do I fix database errors?

Database errors occur as a result of an error when writing or establishing a db connection. This is frequently caused by the most recent database change. To change downgrade database to previous saved version.

#####In Terminal Run...

flask db downgrade

Note: Before you run another migration, Old Migration MUST be deleted first. You can do this easily in terminal by running... (The migrations.py file can be found in the migrations folder in the project's base_dir)

rm -r enter_migration_name_here.py

Validation

To test the accuracy of our web-software, we have manually counted immunogold particles across TEM images of suspended AL aggregates. Here's a more detailed description of amyloid light-chain (AL) amyloidosis.

[AL] M	Total TEM Images Processed	Manual Counts	Particles Detected	FP	FN	Accuracy
3.7x10-6	100	TBD	4894			TBD
3.7x10-8	102	TBD	TBD			TBD
3.7x10-10	100	TBD	TBD			TBD
3.7x10-12	100	TBD	TBD			TBD

• Original dimensions of the processed .tif images were (x,y ) = (2444,3744). This was reduced to (664, 1018) during picking
• The web app was made to be a semi-automatic open-source dot counting platform. To validate the quality of picking & processing, external unrelated dataset of graphs were used.