Basic Navigation in Fiji

Introduction

Fiji contains many different features, menus and plugins. The following is a brief overview of getting around in the Fiji interface.

NOTE: All examples in this chapter use the image H and E 01.tif that can be found in the folder Demo Images\Widefield Images\H and E

Opening Files

This is pretty straight forward. You can either go to File 🡪 Open and then navigate to the file you want. 

Alternatively, you can just drag and drop a file from explorer/finder etc. onto the Fiji window and it will open. 

NOTE: On Windows systems files can be dragged to anywhere on the Fiji bar. For Mac systems the file must be dragged to the blank area in the bottom 3rd of the bar below all the buttons.

Zooming In and Out

To zoom in or out select the Zoom Tool 

To Zoom In left click on the image, to Zoom Out right click on the image or use the + and – keys. Also left clicking while holding down the Alt key will zoom out

Panning the Image

If you have zoomed in a lot, or your image is a higher resolution than your screen can show, you will only be seeing part of the image on your screen. To move to other parts, you need to use the Hand Tool.

Select the Hand Tool and hold down the left button on your image and move the mouse to pan around. You can also hold down the spacebar to activate the hand tool.

When you are zoomed into an image more than what the screen/window can show an overview icon is shown in the top left corner to let you know where you are in the original image.

Duplicating an Image

Sometimes it is useful to work on a copy of an image instead of the original as Fiji doesn’t always create result images; instead it overwrites the original image. Unless the result is saved the original data stays intact but it can be useful to have to original to refer to.

To duplicate an image just right click on it and select Duplicate…. from the menu

In the resulting dialog you can give the image a new name or accept the default which is the original image name with –x on the end of it. 

NOTE: If a region of interest (see below) is drawn on the image first only the part of the image in the region will be duplicated. This is useful for cropping images.
NOTE: A quadrilateral ROI (circle, oval, freehand) will duplicate the image that fits in the extreme boundaries of the shape giving and will not blank out what is outside the ROI.

Regions of Interest (ROI)

There are many instances where you may need to draw a ROI on an image. They can be used to crop an image (by drawing one and duplicating the image) or to highlight a specific area for further analysis.

To draw a ROI select the desired shape. ROI buttons that have a red triangle on them have several variants of that shape available. To access these right click on the ROI button and select the variant from the menu.

Types of ROIs

There is a range of ROI shapes and functions available. Those that have a red triangle at the bottom right of their button have several variations available. To access these, you need to Right Click on the button. Some ROI tools such as the line tool and wand tool have additional functions that can be accessed by double clicking on the button.

Rectangle Tool

Useful for outlining large areas, extracting or cropping part of an image.

Circle Tool

Similar to the rectangle tool but for circular selections

NOTE: Duplicating images with a circle selection will result in a rectangular image.

The circle tool also contains an option called Selection Brush Tool. This tool has additional settings that can be accessed by double clicking on the button. The number in the Size: box indicates the width in pixels of the circle that will be draw. This circle can then be used to “paint” on a selection 

Polygon Tool

The polygon tool allows you to draw irregular shaped ROIs. Just click all the points you need around an area, double click to close the shape off

Freehand Tool

The freehand tool allows you to draw any shape you like. Just hold down the mouse button and draw away.

Line Tool

The line tool allows you to draw line selection as either a straight single line, a segmented line (like the polygon tool but not closed off, a free hand line (like the freehand tool but not closed off) or an arrow for annotations.

The line tools (straight, segmented and freehand) also have an option when you double click on the button to set the width of the line. This is useful when you are measuring intensities along a line as everything is averaged across the width you set to smooth out noise and inconsistencies. 

The arrow tool also has a double click option that lets you to set sizes and styles of the arrow. 

Angle Tool

The angle tool allows you to measure the angle between two lines. Clicking the mouse adds the first point of the ray, the second click marks the vertex and the third click marks the end of the second ray.

To measure the angle you need to use the measure function by going to Analyse 🡪 Measure or pressing Control + M

Double clicking on the angle button brings up an option window that allows you to choose to measure the reflex angle instead (the larger of the two angles).

Point Tool

The point tool allows you to mark an individual or multiple points on an image to measure the XY coordinates and the intensity under the point.

The tool has a right click option to choose between single point and multi points. Once points are marked they can be measured using the Analyse 🡪 Measure command or the Ctrl + M shortcut

The Single point tool has a double click dialog option that allows you to change the style and colour of the pointer as well as the option to automatically add the results of a click to the result table, move to the next slice, add to overlay and ROI manager. 

The multipoint tool also has a double click menu that has less options but can be used as a simple click counter if required (instead of logging data out to a table) 

The Wand Tool

The wand tool allows automatic selection of an area based on a tolerance or threshold value. To use the tool, click on an area you wish select. It may not select it correctly initially but its sensitivity can be adjusted by changing the tolerance value in the dialog that can be accessed by double clicking on the want tool button.

The wand tool has an option to smooth to a threshold if one is on the image. This uses the initial value for the tolerance to select and area and then refine it to the outline the threshold covers. 

Drawing ROIs

To draw the selected ROI hold down the left button on the image and draw as required. If you require more than one ROI hold down the shift key and draw any additional ROIs required.

NOTE: When additional ROIs are added using the shift key they essentially become one big ROI, even if they do not overlap. This means that anything within them will be analysed together. If individual ROIs are needed you need to use the ROI manager to add multiple, separate ROIs. 

Removing ROIs

To remove the most recent ROI you have drawn just click away from it using any of the ROI tools or use the shortcut key Ctrl + Shift + A

Copying/Moving ROIs to Another Image

There are situations where you need to draw and ROI on one image/channel and then use it to measure something in a separate image/channel. To do this draw the ROI then select the image you with to copy/move it to and press Ctrl + Shift + E

Moving ROIs

To move an ROI have any of the ROI tools selected and click and hold inside the ROI

Resizing ROIs

To resize an ROI have an ROI tool selected and click and hold on any of the anchor point around the ROI to adjust its size. 

Holding down different keys while resizing will have different effects on the resizing.

Shift – Will resize the ROI symmetrically. If the ROI was a rectangle or an oval it will become a square or circle with an initial width the same as the width of the ROI.

Ctrl – Free resize around the centre of the ROI

Alt – Resize the ROI while keeping the aspect ratio the same

NOTE – Combinations of keys can be used too. For example hold down Alt and Ctrl to resize an ROI with the same aspect ratio around its centre.

Using the ROI Manager to add Multiple ROIs

To add multiple ROIs to an image they need to be individually added (either manually or by a analysis module) to the ROI manager

1. Go to Analyze 🡪 Tools 🡪 ROI Manager to open the ROI manager

2. Draw an ROI and press the Add button on the ROI Manager (or press the T key). The ROI will be listed in the ROI manger. The label represents the Y and X coordinates of the centre of the ROI

3. Follow the above step to add additional ROIs. If you want to see the previously added ROIs you may need to click the Show All box.

To delete regions, press the delete key. If a region is selected in the list this will only delete the selected region. If no regions are selected it will delete all of them.

You can also select groups of regions by holding down the control key and clicking on them.

ROIs can be saved by selecting More>> 🡪 Save… and restored by selecting More>> 🡪 Open… or by dragging and dropping the roi/zip file into Fiji.