User's Guide

Download

The first step to using GoFigure is to Download it. Please choose the Linux, Mac, or Windows installation packages for the easiest install. You can also compile GoFigure yourself but this is more difficult.

Installation

GoFigure can be run on any computer.  Laptops are fine for working with small image sets, but for serious use it is best to install it on a high-end "workstation" style desktop machine with lots of memory, cores, and disk space as well as a high-end graphics card and one or two big monitors. In the Megason lab most people run it on their laptops for routine use, and we have a few maxed out "gaming style" desktops for more serious work. We prefer Linux over Windows or Mac for workstations as it tends to be more stable, faster, and the user interface is quite nice these days (e.g. Fedora, Ubuntu).

To install GoFigure simply double click on the installation package and follow the instructions. Once installed double-click on the GoFigure icon to load it.

To use all of GoFigure's features, you must also Install MySQL.

Data

The easiest way to test out GoFigure is by downloading our sample data. This data is typical of what GoFigure was designed for so it will best show how GoFigure is supposed to work. You can then try it on your own data.

  • GoFigureSampleData.zip - this file contains 2 frames from an xyzt image set of zebrafish somite development with cell nuclei and membranes in different colors in MegaCapture format. It also contains meshes in the GoFigure eXchange format. Download and unzip the file. Then import the images into the database. Then import the meshes.

Database

GoFigure can do simple visualization of 2d and 3d images without using the database but to visualize 4d images or to use any of the segmentation, tracking, and analysis features, you must use the database. GoFigure uses a database as a backend to manage large image sets comprised of many 2d images in standard formats (tif, jpg, png) organized across various dimensions such as color, depth, and time. To use the database, you must do a one time setup by clicking on "Settings->Database->Set up database" in the menu and following the directions. You can then create "Imaging Sessions" in the database to encapsulate a set of images, contours, meshes, tracks, and lineages. The first time an image set is used in GoFigure, it must be imported into the database as a new imaging session. Subsequently, imaging sessions can be loaded through the database to view the images and previous segmentation results.

To use the above sample data download and extract it on to your computer. In GoFigure, click on "File->Use Database". Login in to the database with localhost and the username/password you chose when you setup MySQL. Choose "Create New Project". Give the project a name and description. Give the Imaging Session a name and description. Choose 1 file from the sample image set by clicking the "browse" button and selecting an image from the megacapture directory. Hitting "Finish" will import all of the image data into the database which may take a few minutes. GoFigure should then show a quad view of the sample image set.

To use the Sample traces, download and extract the file on to your computer. In GoFigure, click on "Tools->Import->3D Meshes". Choose the gfx file and click ok.

Navigation

Image sets are shown in a quad-view comprised of xy, xz, and yz cross-sections along with a 3d view. The x, y,  z, and time locations the cross sections are made at can be adjusted using the navigation window. The x, y, and z locations can also be adjusted by left clicking the section lines in the image views. The 3d view can be rotated by left clicking, zoomed by right clicking, and panned by middle clicking. Use control, shift, and command keys on Mac.

Segmentation

Manual segmentation to make contours (2d shapes) can be done by clicking on the pen button, clicking around a shape of interest, and then clicking the validate button. Meshes (3d shapes) are made by selecting a group of contours and then linking them together by choosing "make mesh out of selected contours". Likewise, tracks (4d shapes) are made by linking together a group of meshes, and lineages (4d+mitosis) are made by linking together a group of tracks.

Semiautomatic segmentation to make meshes is done by placing seed points and then clicking the segment button.

Automated segmentation can be done in GoFigure using the segmentation menu or can be performed on a cluster and then imported to GoFigure using "gfx" segmentation file format.

Analysis

Cell based data for all traces (contours, meshes, tracks, or lineages) can be viewed in the table. This data can be cut and paste into other programs. Traces can be resorted by left clicking the column header and color coded by right clicking on the column header.