Software

Alcian Blue Goblet Cell Measurement - ImageJ Macro

Monash University
Matthew Rowe (Aggregated by) Myat Noe Han (Aggregated by)
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ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=info:doi10.26180/28218062.v1&rft.title=Alcian Blue Goblet Cell Measurement - ImageJ Macro&rft.identifier=https://doi.org/10.26180/28218062.v1&rft.publisher=Monash University&rft.description=This macro will automatically measure the number of goblet cells from Alcian blue stained histology images using a custom trained Cellpose 2.0 model. Specific regions of intact mucosa were defined for analysis by importing predefined ROIs created in QuPath. Additional macro information is commented within the ImageJ Macro script.The script was written on ImageJ Version 1.54f.The following plugins are required:BIOPImageJTS Tools (installed from: https://github.com/petebankhead/imagejts-tools)Additionally, a Cellpose python environment must be installed on the computer to make use of the Cellpose function through ImageJ.The ImageJ Macro was written by Matthew Rowe ([email protected]) in collaboration with Myat Noe Han ([email protected]).&rft.creator=Matthew Rowe&rft.creator=Myat Noe Han&rft.date=2025&rft_rights=CC-BY-4.0&rft_subject=ImageJ Analysis&rft_subject=Cellpose&rft_subject=Fiji Macro&rft_subject=Alcian Blue Staining&rft_subject=Goblet Cells&rft_subject=Image processing&rft.type=Computer Program&rft.language=English Access the software
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CC-BY

CC-BY-4.0

Full description

This macro will automatically measure the number of goblet cells from Alcian blue stained histology images using a custom trained Cellpose 2.0 model. Specific regions of intact mucosa were defined for analysis by importing predefined ROIs created in QuPath. Additional macro information is commented within the ImageJ Macro script.

The script was written on ImageJ Version 1.54f.
The following plugins are required:

  • BIOP
  • ImageJTS Tools (installed from: https://github.com/petebankhead/imagejts-tools)

Additionally, a Cellpose python environment must be installed on the computer to make use of the Cellpose function through ImageJ.

The ImageJ Macro was written by Matthew Rowe ([email protected]) in collaboration with Myat Noe Han ([email protected]).

Issued: 2025-01-20

Created: 2025-01-20

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Subjects
Alcian Blue Staining | Cellpose | Fiji Macro | Goblet Cells | Image processing | ImageJ Analysis |

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Identifiers
ACN 633 798 857