Name Version Author's Type Requirements Brief description Keywords
Name Version Author's Type Requirements Brief description Keywords
NO ICON SaveLasXFileToHyperstack v0.2 Mafalda Sousa mafsousa@ibmc.up.pt Advanced Light Microscopy,i3S - Instituto de Investigação e Inovação em Saúde Script/Macro Imagej/Fiji 1.53 Input LasX isolated tiff files, search for region/positions, stages and create hyperstack for each one, (xyzct). Save as tiff. lasX,hyperstack,imageJ
NO ICON Get Parasite Position from ToAst v1.0 Mafalda Sousa mafsousa@ibmc.up.pt Advanced Light Microscopy,i3S - Instituto de Investigação e Inovação em Saúde Script/Macro Requires python 3.8, tkinter Reads logfile from ToAst (imageJ plugin) output and extracts all the lines until line = "Overall" and saves the tracking number, slice, X and Y position python,Tracking,ToAst
NO ICON Randomize Labels 0.1 Eduardo Conde-Sousa econdesousa@gmail.com INEB - Instituto Nacional de Engenharia Biomédica Script/Macro IMAGEJ If one labeled image has too many labels, "glasbey on dark" will not properly (visually) separate neighbours. This macro randomizes labels so two neighbours have little chance of having close values. label image,random
NO ICON Mitochondrial stats 1 Eduardo Conde-Sousa econdesousa@ineb.up.pt INEB - Instituto Nacional de Engenharia Biomédica Script/Macro ilastik Mitochondrial segmentation and classification into puncta, rods, or networks Mitochondrial
NO ICON Meta Data Viewer and Editor 0.1 Eduardo Conde-Sousa econdesousa@ineb.up.pt INEB - Instituto Nacional de Engenharia Biomédica IMAGEJ Meta Data Viewer and Editor metadata
NO ICON getDistInPixels 0.1 Eduardo Conde-Sousa econdesousa@ineb.up.pt INEB - Instituto Nacional de Engenharia Biomédica IMAGEJ get distance, from a line tool selection, in calibrated units as well as in pixels. distance
NO ICON CountNucSTARDIST 0.1 Eduardo Conde-Sousa econdesousa@ineb.up.pt INEB - Instituto Nacional de Engenharia Biomédica Script/Macro Stardist Use StarDist to count number of nuclei Stardist
NO ICON 3D Cell density assessment 0.1 Eduardo Conde-Sousa econdesousa@ineb.up.pt 3S - Insttuto de Investgação e Inovação em SaúdeINEB - Insttuto Naconal de Engenhara BomédcaINEB - Insttuto Naconal de Engenhara Bomédca ilastik plugin CLIJ2 ClIJx * 3D cell segmentation from DAPI channel using ilastik pixel classification workflow * Cell type evaluated from other channels * output * Cell density map (DAPI) * Cell density map (other markers) 3D
NO ICON Stardist_process_folder v0.1 Mafalda Sousa mafsousa@ibmc.up.pt Advanced Light Microscopy,i3S - Instituto de Investigação e Inovação em Saúde Script/Macro Run on ImageJ/Fiji v1.53 Install plugin StarDist from the update sites select CSBDeep and StarDist This is a generic macro to apply a pre trained StarDist 2D model to a folder of images DL,Stardist
NO ICON CreateBandsQuadrants. v0.1 Mafalda Sousa mafsousa@ibmc.up.pt Advanced Light Microscopy,i3S - Instituto de Investigação e Inovação em Saúde Script/Macro ImageJ/Fiji v1.53c Creates "sholl analysis" concentric shell with a specific number/width of bands from a starting Roi ROIs; quadrants
NO ICON ChangeFilenames v1.0 Mafalda Sousa mafsousa@ibmc.up.pt Advanced Light Microscopy,i3S - Instituto de Investigação e Inovação em Saúde Script/Macro python > = 3.6, PySimpleGUI Allows changing filenames and/or removing spaces in a specific folder python,batch
NO ICON AppendExcelfiles v0.1 Mafalda Sousa mafsousa@ibmc.up.pt Advanced Light Microscopy,I3S Requires python 3.8, pysimplegui ('python -m pip install pysimplegui') and pandas (python -m pip install pandas) The script will append excel files with the same columns and save one excel file with the result excel; python
NO ICON 2p_FFT 1.0 Gabriel G. Martins gaby@igc.gulbenkian.pt IGC - Instituto Gulbenkian de Ciência;
Nuno P Martins nuno.pimpao@gmail.com 		Fiji ImageJ macro to correct jagged stripes created by electronic noise (visible in our 2P/Multiphoton system), using a Fast Fourier Transform to detect maxima on the FFT image and then eliminate high freq bands. FFT
NO ICON ToxoGauge 0.1 Gabriel G Martins gaby@igc.gulbenkian.pt Instituto Gulbenkian de Ciencia Script/Macro requires ImageJ/FIJI Measures semi-automatically size and fluorescence in Toxoplasma gondii parasites in cell cultures Toxoplasma,fluorecence quantification
NO ICON CziToTiff 1.0 José Serrado Marques jpmarques@igc.gulbenkian.pt IGC - Instituto Gulbenkian de Ciência Fiji, Bio-formats Converts .czi into .tif files. this macro goes through folders and subfolders searching for .czi files to process. saves the .tif files in the same folder structure. Works for split positions and single files. Fiji,Macro,CziToTiff
NO ICON DIC_Illumination_Uniformization 1.0 José Serrado Marques jpmarques@igc.gulbenkian.pt IGC - Instituto Gulbenkian de Ciência Fiji. RGB images Macro to uniformize brightness for all DIC images using Retrospective (a posteriori) correction. Useful to have images ready for publication. Fiji,macro,DIC
NO ICON add overlay to from 16-bit labeled image. 0.1 Eduardo Conde-Sousa econdesousa@gmail.com INEB - Instituto Nacional de Engenharia Biomédicai3sINEB - Instituto Nacional de Engenharia Biomédicai3S - Instituto de Investigação e Inovação em Saúdei3S - Instituto de Investigação e Inovação em Saúdei3S - Instituto de Investigação e Inovação em SaúdeINEB - Instituto Nacional de Engenharia Biomédica;
Eduardo Conde-Sousa 		ImageJ and Ilastick plugin 16bit LUT for label masks LUT; overlay; label mask
NO ICON Quantification of protein expression in dark patches 2 José Serrado Marques jpmarques@igc.gulbenkian.pt IGC - Instituto Gulbenkian de Ciência Script/Macro Requires Fiji Quantification of Cy5 protein expression in dark patches. ImageJ,Quantification,Fiji,macro
NO ICON NeuronRead 1.1 Roberto Dias roberto.dossantosdias@kuleuven.vib.be VIB & KU Leuven Center for Brain & Disease Research;
Sandra Vieira sivieira@ua.pt iBiMED, Universidade de Aveiro		 Script/Macro Requires ImageJ, with MorphoLibJ v1.2.0, Skeletonize3D and AnalyzeSkeleton installed. NeuronRead is an interactive semi-automated image processing workflow developed to extract relevant information (e.g. total neuritic length, average cell body area) from both Phase Contrast and Fluorescence neuronal images. ImageJ; Neuronal Images; Phase Contrast; Morphological analysis
NO ICON FretRatiometric c0x.x Mafalda Sousa mafsousa@ibmc.up.pt IBMC - Instituto de Biologia Molecular e Celular,i3S - Instituto de Investigação e Inovação em Saúde ImageJ; ImageJ plugin Polynomial Shading Corrector FRETRatiometric is composed by three macros: FRET_ratiometrics_v0x.x, the main macro for FRET analysis; NormalizeHistogramForPrinting, for normalizing the resulting images for printing proposes and Create_HSB_Image, to create an HSB image with the FRET output. It allows calculating FRET ratiometric between donor and Acceptor channels along time or on a specific time-point. imagej; fiji; fret; fretratiometric
NO ICON Wound-healingArea v1.0; October 2020 Mafalda Sousa mafsousa@ibmc.up.pt IBMC - Instituto de Biologia Molecular e Celular,i3S - Instituto de Investigação e Inovação em Saúde Script/Macro ImageJ/Fiji Measure the wound-healing area along time or for one frame imagej; fiji; woundhealing; segmentation
NO ICON Radially_spatial_cell_measurements v0.2; November 2019 Mafalda Sousa mafsousa@ibmc.up.pt IBMC - Instituto de Biologia Molecular e Celular,i3S - Instituto de Investigação e Inovação em Saúde Script/Macro ImageJ; IJPB-plugin (https://github.com/ijpb/MorphoLibJ) Calculate intensity around border cell band(s) imagej; fiji; cellprofiler
NO ICON Count Cells Over Fibers 0.3 Eduardo Conde-Sousa econdesousa@gmail.com INEB - Instituto Nacional de Engenharia Biomédica,i3S - Instituto de Investigação e Inovação em Saúde Script/Macro ImageJ Segment fibers and then count number of cells over them. Blob Counting,Fibers
NO ICON Import ROI Files From Andor IQ | AndorRegionImporter 1 Pedro Almada IGC - Instituto Gulbenkian de Ciência Script/Macro Andor IQ, ImageJ/FIJI This macro let's you import .rgn files created with Andor iQ. Regions are added to the ROI Manager. IQ,ROI,FRAPPA
NO ICON Centromere Recognition And Quantification | CRaQ 1 Nuno Moreno moreno@igc.gulbenkian.pt IGC ImageJ The macro recognizes centromere or kinetochore foci in Delta Vision or TIFF images and determines their centroid position. Fluorescent intensities are then measured for each centromere by placing a small box around the centroid position of the centromere. The peak intensity value within the box is corrected for local background by subtraction of the minimum pixel value. This process results in an accurate measurement of large numbers of centromere or kinetochore-specific signals. Centromere,macro,Quantification,IGC
NO ICON LIF to TIFF v0.3/Nov 2019 Mafalda Sousa mafsousa@ibmc.up.pt IBMC - Instituto de Biologia Molecular e Celular,i3S - Instituto de Investigação e Inovação em Saúde Script/Macro ImageJ v1.52p This macro will open Lif files from a specified folder and save every series inside the Lif as a separate tiff stack file. Lif,Tiff,Fiji,ImageJ,FileConversion
NO ICON intramacrophagic parasites counter v00 (IN Cell Developer), v01 (CellProfiler) André Maia andre.maia@i3s.up.pt IBMC - Instituto de Biologia Molecular e Celular,i3S - Instituto de Investigação e Inovação em Saúde CellProfiler 3.0 or higher IN Cell Developer Toolbox 1.9 or higher Automated image analysis protocol to count intracellular parasites. Parasites and Nuclei are segmented from the same DAPI channel. segmentation,nuclei,cells,particles,intracellular,cellprofiler,incell
NO ICON From In Cell To Hyperstack V0.2 - Out/2019 Mafalda Sousa mafsousa@ibmc.up.pt IBMC - Instituto de Biologia Molecular e Celular,i3S - Instituto de Investigação e Inovação em Saúde ImageJ v1.52p Create a hyperstack for each field within each well for InCell High-Throughput system files. InCell,Hyperstack,Fiji,ImageJ