BioImage Analysis tools

Simple bioimage analysis macro/scripts developed at Advanced Light Microscopy Facility at I3S, Porto Portugal

ImageJ/Fiji

• LIFtoTIFF: Convert the series of a LIF file into TIF format

• FromInCellToHyperstack: convert InCell images in hyperstack arranged by wells and fields

• SaveLasXFilesToHyperstack: convert Leica isolated images in hyperstack arranged by position/region/field

• Woundhealing_TimeSegmentation: calculate wound healing area of a time-lapse image

• StarDist_process_folder: apply a pre trained StarDist 2D model to a folder of images

• CreateBandsQuadrants: creates "sholl analysis" concentric shell with a specific number/width of bands from a starting Roi

  

• SetParasiteLabel: creates an annotated image with the parasite track information obtained from GetParasitePosition.py script

Python

• InCell_Merge_Excel_Files: merge at least two excel files from InCell analysis results

• From_subfolder_to_folder: join files from different subfolders to he same level folder

• ChangeFilenames: change file names, by string replacement. Also allows removing file name spaces(e.g, test 1.txt to test1.txt)

• MergeExcelFiles: Merge two excel (.csv) files (source and target) by specifying the columns number to copy from source to target file;

• AppendExcelFiles: Merge excel files with the same columns and save in a new excel file;

  

• GetParasitePosition: Extract tracks position information from logfile.txt (the output of the ToAsp plugin https://imagej.net/ToAST)

Authors

Mafalda Sousa, BioImage Analyst, [email protected]

Licence

Explicit acknowledgement to the ALM facility should be done in case of published articles (approved in C.E. 7/17/2017):

"The authors acknowledge the support of i3S Scientific Platform Advanced Light Microscopy, member of the national infrastructure PPBI-Portuguese Platform of BioImaging (supported by POCI-01-0145-FEDER-022122)."