2017-01-16 Author: Nicolas Stifani [email protected]
This is a plugin for ImageJ intended for Processing, Manual Registration and Cell Count of spinal cord images. It requires ImageJ 1.50 and above.
To install it:
- Download the Spinalcord_Mapper.jar
- Save it into your Folder ImageJ\plugins\
- Restart ImageJ You will find the function into ImageJ Menu > Plugins > Spinalcord Mapper
General Requirements − Image Files should be TIF, named with the following nomenclature DATE_ANIMAL_GROUP_OTHER_VARIABLES_SEPARATED_BY_UNDERSCORE.TIF − The files should contain only one “.” character for the file extension. − Each variable should be separated by a “_” − Do not use _ unless for separating variables − Do not use special characters such as ~!@#$%^&*”’;:<>?/|
1.1 Spinal cord Registration with Spinalcord Mapper 1.1.1.1 Installation − TIF files should be in a single folder − Images should be aligned so the dorso-ventral axis is roughly vertical − Download Spinalcord_Mapper.jar from https://github.com/nstifani/Spinalcord_Mapper − Save Spinalcord_Mapper.jar in your ImageJ/plugins folder and restart ImageJ 1.1.1.2 Registration − Open ImageJ − Select Plugins/Spinalcord Mapper/SC Registration
Select the folder containing the TIF files − Click sequentially on the Central Canal, the Dorsal Edge of the Right side, the Lateral Edge of the Right side, the Ventral Edge of the Right side, the Ventral Edge of the Left Side, the Lateral Edge of the Left side, the Dorsal Edge of the Left side of the grey matter − Spinal cord Mapper will save for each image: o a TIF file with the Registration Points as an overlay o the Registration Points as a Region of Interest ZIP file o the X and Y the Registration Points Coordinates in a CSV File