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.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).
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