README.md

To use SCC on Colab, go to the following link:

https://colab.research.google.com/drive/1ZC5GXTEnJ5V3ZIPfcw_uvb9S4eJgbule?usp=sharing

(1) Create Gmail if you do not have one

Ensure a basic familiarity with Google Drive

(2) Open Files

Open scc_colab and select the banner at the top of screen Open in Colab

(3) Set Up Colab

First begin by selecting Runtime then Change runtime type, then under Hardware accelerator select GPU

(4) Begin Running Code

(a) Initialize Session

This section imports all the relevant packages

Note: Tensorflow 1x is used here for accurate inference since the original CNN model was trained on Tf 1.0

(b) Connect Drive to Colab Session

This section makes your google drive accessible to Colab...once this code is run, a link will appear:

- click this link and follow the prompts until you receieve an authorization code.

- paste the authorization code into the Colab notebook prompt and hit Enter

(c) Clone SCC into Drive

Run this block to copy the SimpylCellCounter repository into the My Drive folder in your drive

(d) Upload Images into Drive

- navigate to My Drive in your Google Drive

- select New -> Folder Upload and upload your image data

(e) Run Main SCC Script

This code block executes scc

(f) Save Output

This code block will save the output of SCC under My Drive in your drive with the title scc_output followed by the date and time