ROF filter based macrophage segmentation in IHC stained tissue samples: MATLAB procedures
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This is a set of MATLAB procedures for automated segmentation and counting of macrophages in multiple IHC stained tissue samples.
Execution assumes that three aligned single-channel greyscale images of a given tissue area are available, representing IHC stainings with CD14 and CD163 antibodies (targeting macrophages) as well as DAPI staining (targeting cell cores). After detection of evaluation subregion (based on DAPI channel information), IHC stained macrophages will be masked and counted (based on information from CD14 and CD163 channels). To start the analysis, type rofsegmpublicstep00masterfile within the MATLAB command window. You will be asked to enter the image filenames and to confirm the parameter settings. Progress of segmentation can be traced by display messages. Parameters can be modified within the file rofsegmpublicstep01parameters.m. Possible modifications of the basic procedure in order to enforce batch processing are left to the user.

Health Atlas ID: 7W1Q4R1TN6-6

1 item is associated with this Model:
  • yf_rof_segm_2019_04_15.zip (Zip file - 1.32 MB) Download

Organism: Not specified

Human Disease: Diffuse large b-cell lymphoma

Model type: Not specified

Model format: Matlab package

Execution or visualisation environment: Matlab




Model image: No image specified

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Views: 1335   Downloads: 95

Created: 13th May 2019 at 15:23

Last updated: 23rd May 2019 at 12:54

Last used: 28th Feb 2021 at 15:46

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