Software - FIJI
FIJI (FIJI is just ImageJ)
- Free open source image processing package
- Opens all our native file formats
- Compatible with Windows, Mac and Linux
- FIJI is a version of ImageJ that will automatically update and load a variety of useful plugins including the Bio-Formats Importer
- View and edit original image file formats
- Measurements and analysis tools
- Image presentation
- Wide selection of plugins
- Macros and macro writing
FILM staff can provide FIJI training and help with macro writing
We have a written a few macros to help with presentation and analysis which you can download
(download and save the text file to the macros\toolsets directory of FIJI. It can then be loaded by selecting it using the >> on the FIJI toolbar)
Download the file Macros (ZIP) containing all the macros and unzip it to the FIJI directory under the subdirectory of macros/toolsets.
The Macro Toolsets can then be selected by clicking on the >> on the tool bar.
LUT (look up table)
you can also download the "Light Blue LUT" LUT, unzip and save it to the luts subdirectory of FIJI
Macro Update History
These macros are updated regularly (either use the macro update tool (Calibrate and Batch tools - you have to be a member of FILM and be on the college network or re-download the latest version from the link above).
- A new tool to calibrate the re-sampled images from the Bio-Formats importer for tiles where only the full format is calibrated
- A new tool to add a single channel fixed image to a time series (Presentation 2 toolset).
- Lambda intensity tool updated to multi ROI and image projection. New tools to generate LUT's from wavelenth and also from RGB selection (Presentation 2 toolset).
- General update and reorganisation.
- A new tool to create a zoom movie from a single image. Options to add scale bar and mask frame and also the number of images (Presentation toolset).
- A new tool to create an intensity plot that can be joined to an image series displaying intensity changes frame by frame for a single channels (limited to 10 ROI’s) (Intensity Toolset)
- An updated version of the ROI time plot tool to allow more than 15 ROI's to be selected (Intensity 2 Toolset) .
- A new tool to reverse the order of the Z slices in a multichannel hyperstack - also works on a time-Z series (Presentation 2 Toolset) .
- A new tool for creating a colour height map from a Z-stack using threshold. Included are options to add a calibration bar and re-size image (Presentation 2 Toolset) .
- A new tool for creating a colour thickness map from a Z-stack using threshold. Included are options to add a calibration bar and re-size image (Presentation 2 Toolset) .
- A new tool for measureing the area of a Scratch/wound assay image (ROI_Tools Toolset)
- A new tool for inserting a "Inset" Z-Stack into a larger Z-stack eg for changing the output of the 3D Gallery tool (Presentation 2 Toolset)
- A new tool for creating a fancy cytofluorogram using the data produced from the JACoP Co-Localisation plugin (Presentation 2 Toolset).
- A new tool for creating a colour orientation scale for use with images generated using the Orientation J Plugin (Presentation 2 Toolset).
- A new tool to Join together multichannel Z stacks, set LUT's and reset brightness and contrat to Min Max. Useful for loading the de-convolved images from Huygens (Presentation 2 Toolset).
- New toolset "Presentation 2" added to include Image information Tool - creates a graphic summary of the image dataset (Calibrate and Batch toolset) added and aslo an auto brightness and contrast reset tool. Presentation crop tool updated to correct for errors.
- Image information Tool - creates a graphic summary of the image dataset (Calibrate and Batch toolset) added
- Tool for overlaying and combining 2 RGB colour images (Calibrate and Batch toolset) added
- A multi 3D projection tool added (presentation) - Creates a series of rotations from the 3D projection command which are then concatenated into one series. Options for each rotation step (type, axis, direction, start, range, step, etc).
- Simple shade correction tool moved to Intensity 2 toolset
- Ratio time plot tools (single and multi ROI) - combined Intensity and ratio plots with channel select (Intensity 2 toolset) added
- New multiimage Gallery tool (Presentation toolset) added
- Library image split and save tool (.lif and .czi files) (Series toolset) added