TITLE: Algaeorithm Classroom Guide: Analyzing Microscope Images
AUTHORS: Ashwin Mukherjee, rohan chanani

[DESCRIPTION]
A guide to using Algaeorithm to analyze microscope images of algae.

[STEPS]
SECTION: Preparation
1. Before getting started, you'll want to ensure your photos meet the following criteria:
400x magnification (typically through a 40x objective lens)
clear/focused viewfinder
high contrast between the viewfinder and the background

see examples of photos below:
  
SECTION: Uploading Images
2. Once your images have been prepared, head to algaeorithm.com.
SECTION: Uploading Images
3. Click the "add image" button in the top left corner of your workspace to upload your photos; photos should appear as previews here.
 
 
 

SECTION: Uploading Images
4. If unwanted photos are uploaded, hover over them and click the "delete image" button in the top right of the image to delete them.

 
SECTION: Labeling Data
5. The settings area on the right of your workspace is where you'll provide relevant information about your images.

 
SECTION: Labeling Data
5.1. Algae Type

Starting at the top, you can toggle between either Chlamydomonas (represented by the circular green cells) or Phaeodactylum (represented by the banana-shaped beige cells). 

 
SECTION: Labeling Data
5.2. Depth

If all your photos were taken in plates with the same depth, keep the "consistent" option and change the depth (in millimeters) as appropriate.

 
If photos are a mix of plates with varied depths, choose the "varied" option and label each image's depth as appropriate (in millimeters). You also have the option to specify a depth that non-labeled images will default to.

 
SECTION: Labeling Data
5.3. Time

If you have time-sensitive data, you can toggle the "time" switch, enter units manually, and label individual images. You also have the option to specify a regular interval between when photos were taken. 

 
SECTION: Labeling Data
6. Double-check that all relevant images have been uploaded and labeled with accurate information, then click the  "analyze images" button at the bottom.

 
SECTION: Data Interpretation + Analysis
7. Statistical Overview

You'll start with an overview of your data that includes relevant statistics in addition to visual representations of your data.
SECTION: Data Interpretation + Analysis
7.1. The summary area on the left displays the mean, range, standard deviation, median, and interquartile range for your data.

 
 

SECTION: Data Interpretation + Analysis
7.2. The graph area on the right presents visual interpretations of your data in the form of a box plot and histogram. If you input time data, you'll also be able to view exponential, linear, and logistic growth curves. Toggle between these graphs using the labels at the bottom.

 
 

SECTION: Data Interpretation + Analysis
8. Image Analysis

You can switch to the image analysis tab using the floating navigation menu at the bottom of the page. Here, you'll be able to view individual images and explore how Algaeorithm's neural network interprets these images.
SECTION: Data Interpretation + Analysis
7.3. You can also switch the units between cell concentration in cells/mL to absolute cell count for all this information using the slider at the top of the screen.

 
SECTION: Data Interpretation + Analysis
9. Data Table

Using the floating navigation menu, you can switch to the data table tab. This table names each image by its file name and includes any input information (depth, time, etc.) along with calculated cell count and concentration in cells/mL.

 

SECTION: Data Interpretation + Analysis
8.1. Your images are displayed both in their raw form (image) and an algorithm-labeled patch (output). The space on the right displays the cell count and concentration for each image. Rotate through images using the navigation menu above the main image.

 
 

SECTION: Data Interpretation + Analysis
9.1. The "download table" button allows you to save your data table as a .csv file which can be opened in Microsoft Excel or Google Sheets for further analytics, or copied into other documents.

 
SECTION: More Content
10. Using the menu at the top right, you can access pages that host educational content, Algaeorithm's story, and press this project has received.

 
Thanks for using Algaeorithm!