A Fiji (ImageJ) macro written in jython for automated batch analysis of histology sections.
This is a macro written in Jython for Fiji (ImageJ) you must use Fiji because some Pull program into Fiji and press run.
You will be asked to select your input folder. This should contain your histology sections.
The program will run all the images in a folder in a batch applying the same threshold to each image. Create a folder with 3-5 images to test the threshold and then appy these threholds to the larger dataset.
For mouse brain sections the threshold will likely need to be adjusted for each brain region.
The measurements will be compiled into a csv.
Rhalena A. Thomas, Eddie Cai, Vincent Soubannier and Frederick Larroquette
Analysis created for and used in:
Tavassoly O, Del Cid Pellitero E, Larroquette F, Cai E, Thomas RA, Soubannier V, Luo W, Durcan TM, Fon EA. Pharmacological Inhibition of Brain EGFR Activation By a BBB-penetrating Inhibitor, AZD3759, Attenuates α-synuclein Pathology in a Mouse Model of α-Synuclein Propagation. Neurotherapeutics. 2021 Mar 12. doi: 10.1007/s13311-021-01017-6. Epub ahead of print. PMID: 33713002.