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Processing and analysys for Cyclic Immunofluorescence (CycIF) microscopy images
License: MIT License
This project forked from sorgerlab/cycif
Processing and analysys for Cyclic Immunofluorescence (CycIF) microscopy images
License: MIT License
ImageJ & Matlab scripts for processing t-CyCIF files. Key references: 1. Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method JR Lin, M Fallahi-Sichani, PK Sorger - Nature communications, 2015 2. Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes JR Lin, B Izar, S Mei, S Wang, P Shah, C Yapp… - eLife, 2018 in press This work was funded by NIH/NIGMS LSP grant P50-GM107618,NIH LINCS grant U54-HL127365, and NIH STTR grant R41-CA224503. ---------------------------------------------------------------------------------------------------------------------------- System requirement: ImageJ 1.49j or above Matlab 2015a or above Third-Party plugin & software: For ImageJ/Fiji:: TurboReg: http://bigwww.epfl.ch/thevenaz/turboreg/ StackReg: http://bigwww.epfl.ch/thevenaz/stackreg/ MultiStackReg: http://bradbusse.net/downloads.html For Matlab:: Cyt package: https://www.c2b2.columbia.edu/danapeerlab/html/cyt-download.html --------------------------------------------------------------------------------------------------------------------------- Instructions: Step 0: Rearrange your image files (rpcnl files) to one folder, and rename file to Cycle0.rpcnl…CycleX.rpcnl, or use the Matlab rename script we provided (CycIF_rename_rcpnl.m). Step 1: Save induvial frame from different cycles: Run ImageJ macro 1_Macro-SAVEALLCYCLES.ijm. Step 2: Registration: Run ImageJ macro 2_Macro-imagereg-forRareCyte.ijm. Step 3: Segmentation & quantification: Run ImageJ macro 3_Macro-CycIF-wholeSlidequan.ijm Step 4: Import data files to Matlab: Generate a cell array with labels for each channels (plus four additional readings: 'AREA', 'CIRC', 'X','Y'. Then run Matlab script CycIF_readwholeslide.m Step 5. Using "writetable" function to generate CSV files, then you can import & analyze in CYT package.
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