Fiji_Macros by Elisa

SUMMARY

• GENERAL MACROS:

  • run-different-macro.ijm = apply different macros on different files at once
  • Macro_OpenDeconvFiles.ijm = Open all the images in a .lif and keep opened only the wanted one

• CENTRIOLE ANALYSIS (Guichard Hamel Lab)

  • Macro_CentriolesExtraction.ijm = Extract Mother/Dauther centrioles from your .lif file, crop/resize them and save them separately. Thunder or Stellaris versions take into account the different possible deconvoluted files names
  • Macro_CentrioleAnalysis.ijm = Plot profile analysis on centrioles (extracted in .tif) , derived from the "PickCentriole" plugin.

• IMMUNE SYNAPSE

  Old files = made in 2023-2024 in Geneva. Use new files to get latest versions
  

  • Macro_SynapseSegmentation.ijm = Isolate the coated-glass synapses from the .lif files and save the ROIs
  • Macro_SynapseSegmentationCAR.ijm = Same as the previous one but modified to include a rough analysis of isolated synapses (area and circularity)
  • Macro_ActivationState.ijm = Open segmented synapses [from Macro_SynapseSegmentation] and ask the user the activation state according to actin
  • Macro_SynapseAnalysis.ijm = Open segmented synapses [from Macro_SynapseSegmentation] and analyse MTOC polarization AND/OR protein repartition at the synapse
  • MT Analysis:
    • Macro1_MT-Analysis_Normalization.ijm = Open segmented synapses [from Macro_SynapseSegmentation] and get the mean value of a few individual MT selected by the user
    • Macro2_MT-Analysis.ijm = Open segmented synapses [from Macro_SynapseSegmentation] and measure MT network area, total intensity normalized, and integration of an intensity profile
    • Macro_MTQuantifNEW.ijm = Open segmented synapses [from Macro_SynapseSegmentation] or [from Macro_SynapseSegmentationCAR] and measure MT total intensity normalized by the background mean intensity (no need to define individual MT)
  • Macro_GranulesAnalysis.ijm = Open segmented synapses [from Macro_SynapseSegmentation] and analyse Mitochondrial signal in granules indentified by NHS staining (on Z projection)
  • Macro_MitochondriaAnalysis.ijm = Open segmented synapses [from Macro_SynapseSegmentation] and analyse Granules in 3D
  • Conjugates:
    • Macro_ConjugatesExtraction.ijm = Isolate the conjugates manually selected by the users from the .lif files and save the ROIs. Save each individual synapse with right orientation and colors as a .tif file in separated folder.
    • Macro_ConjugatesShape.ijm = Open isolated conjugates [from Macro_ConjugatesExtraction] and measure solidity and deformation at the synapse
  • Macro_NucleusExclusion.ijm = (Macro for Hermine) Segment cells and nucleus using BF/Actin and DAPI and measure 1 channel intensity in cytoplasm vs nucleus