Getting Started

This tutorial explains how to use Quantius to analyze your images. If you're new to Quantius, you might want to start with the explanation of how it works.

If you have any questions along the way, feel free to email help@quanti.us.

Prepare your images

The first step is to save your images in a folder on your computer.

Typically, you would start with an image stack from an experiment and save the individual frames as separate image files. For instance, in FIJI, you could click File > Save as > Image sequence. Quantius accepts these common image formats: .jpg, .png, .gif, and .tif.

Avoid making your images too big or complicated. You should be able to analyze a single image with fewer than fifty clicks. Images should be less than 1000px wide.

Start a job and upload your images

In the upper-right corner, click the green button labeled Create New Job.

Give your job a name. Then, click Add images and select the images you want to analyze. If you have lots of images, this could take a few minutes.

Choose a tool

Next, choose a tool:

  • Crosshairs: click individual objects. This tool is useful for counting and determining the position of discrete objects like cells, beads, cilia, neuronal synapses, organelles, and liquid crystals.

  • Polygon: draw shapes around objects. This tool is useful for determining the area, perimeter, number, and position of objects like spreading cells, tumor tissue borders, electron microscopy particles, and animal morphological features.

  • Freehand: this works like the polygon tool, but it lets the user trace a shape with the mouse, rather than click points to create a polygon.

  • Line and multiline: draw lines or several connected lines. This tool is useful for tracing or measuring the length of objects like material fibers, actin filaments, and microtubules.

You can also use the slider tool in combination with any of the tools above. The slider lets workers click forward and backward through a series of images. The slider is useful when you want to track objects through time or space. Images will be displayed in order of the filenames—so, for instance, image-1.jpg will be displayed before image-2.jpg). We recommend naming your files numerically (like 001.jpg, 002.jpg, etc.).

Add instructions

Describe how you want your images to be analyzed. Here are some rules of thumb:

  • Someone with no scientific training should be able to understand the task.

  • Be clear and concise. We recommend 1–3 sentences in plain English.

  • Don't require too many clicks per image. It should take fifty clicks or less to analyze one of your images.

Here are some examples of good instructions:

  • Click the center of each green shape. Don't click the pink shapes.

  • Click each toe on the mouse's feet.

  • Trace the outline of the smooth shape. If the edge is unclear, make your best guess.

Simpler is better. How would you explain it to a stranger with no special training? If possible, ask a non-scientist friend to read your instructions.

Replicates

A replicate is a human analysis of an image. For instance, five replicates means that each of your images will be analyzed by five different people.

For accurate results, we recommend at least three replicates. If your images are complicated or ambiguous, we recommend at least five to ten.

Why? Quantius is based on collective intelligence: when many humans analyze the same image, we combine their input and automatically filter out bad data. More human input means more accurate results and fewer errors.

Test Mode

Test mode lets you try a job and share it with friends. Test jobs are free. You will receive an email with a private link to your job.

Crowd workers will not see test jobs. If you want to test how crowd workers perform, do not use test mode. Instead, load a regular job, look at the data you get back, and adjust the job as needed.

Start your job

Review your job. Have you uploaded the right images? Are the instructions correct? When you're ready, click Create job. You'll be prompted to enter your credit card number. (If you're running the job in test mode, you will not need to enter a credit card number.)

After that, Quantius will start working on your images. Most jobs take one or two days, but sometimes jobs are finished in just a few hours. You'll get an email when your results are ready.

You can download your data as a CSV file (i.e., a spreadsheet) or as a JSON file. Coordinates are measured from the bottom left corner.