Moved some macros to other toolsets to rationalise them.A new macro to add a fxed image to a Lambda colour coded time series (Presenation 3 toolset).A new toolset containing several tools for genereating ROI's (ROI_Mask toolset).2 new macros added for measuring distances between ROI's (ROI_Mask toolset).a new macros added for shade correction using a reference image (Intensity 2 toolset).a new macros added to create uniform ROI's from points or ROI's in the manager (ROI_Mask toolset).a new macros added for measuring distances between a singfle target ROI and multiple source ROIs in 3D (ROI_Mask toolset).a new macros added for measuring distances between source and target ROI's in multichannel images (ROI_Mask toolset).a new macros added to create ring ROIs from combined original ROIs (ROI_Mask toolset). a new macros added - Difference of Gaussians for edge detection(Extras toolset).a new macros added - a variation of the Bleach Correctin plugin (Series toolset).a new macros added - a macro that will save individual slices of a stack named numerically (Extras toolset).a new macros added - a macro that will create a quick grahic data plot from an existing results table (Extras toolset).a new macros added - This macro allows adding and moving of graphics in each frame of the movie.NB use the plugins link to the Bio-Formats Importer when opening the image not “File Open”. Macro added - This macro will read the time interval and extract the time frame data from a line scan LSM file format image.(It currently only works on a time or Z series, not both) (Presentation 2 toolset)a new macros added - This or by grouping sequential projections eg 1-5, 6-10, 11-15. Macro added - This macro will create a new enhanced stack either by grouping a rolling projection around each image slice/frame eg 1-5, 2-6, 3-7.a new macros added - This macro generates a Weibel grid (a line grid distribution based on an equilateral triangle).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). Download the Colour Deconvolution Vectors (ZIP) text file and save it to the "plugins" subdirectory of FIJI. You can also download our user-created additional vector sets ( Picrosirius red - 2 options, and additional Massons Trichrome for darker samples and a Massons Trichrome for a black background and Alcian Blue PAS). Download the file, unzip and save it to the luts subdirectory of FIJI. You can also download some useful Look-up tables ( FILM LUTs (ZIP)) : Light Blue, Heat Map, Leica Glow, Height and BCGYRM Spectrum. Determines the average total intensity per field.ĭownload slides from the "Macro Writing Tutorial" Macro Tutorial Slides (PDF) LUT (look up table) This macro was specifically created for endothelial colony forming cells (ECFCs) but may be suitable for analysing flourescence in other cell types. Cell contraction: Cell Contraction Analysis (ZIP) Dr Blerina Ahmetaj-Shala and Prof Jane Mitchell (NHLI, Imperial College London) to investigate whether cells derived from smooth muscle progenitors can contract. Determines the change in total area, length and width of selected cells over time. Ĭell fluorescence intensity: Cell Intensity Macro (ZIP) A macro designed with Dr Blerina Ahmetaj-Shala to determine the fluorescence intensity of individual cells stained with different markers.The Macro Toolsets can then be selected by clicking on the > on the tool bar. Either unzip the TXT files to the FIJI directory under the subdirectory of macros/toolsets, or save them to a folder, drag the Installer.ijm file onto FIJI and run it, selecting the location of the macro files when requested. We have a written a few macros to help with presentation and analysis which you can download belowĭownload the file Macros (ZIP) containing all the macros and an installer macro ( Installer.ijm). Scientific figure preparation: FigureJ, Scientifig, QuickFigures (needs installing)įILM staff can provide FIJI training and help with macro writing.Deconvolution: DeconvolutionLab 2 (needs installing).Simple Neurite Tracer: SNT (needs installing).Directionality: OrientationJ (needs installing).Co-localization tools: JACoP (needs installing).Spot Tracking: TrackMate (included in FIJI) - useful webinar: ( YouTube webinar).Registration of time/z-stack series (included in FIJI).Colour Deconvolution: analysis of brightfield histological stains (included in FIJI).View and edit original image file formats.FIJI is a version of ImageJ that will automatically update and load a variety of useful plugins including the Bio-Formats Importer.Free open source image processing package.
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