![]() (in folder: "Matlab 3d visualization files") *the Microsoft Excel macro file (in folder: "Excel data organizer macro file").NB 2! Both plugins 1 + 2, including the Excel and Matlab files are automatically installed by adding our update site (see Installation - option 1). NB! This is the repository for Plugin 2 in the above image. I found a good cell counting tool for ImageJ lacking, so maybe this plugin (and plugin 1) can be included as a standard part of FIJI. The ImageJ plugin 1 might be somewhat hard to understand how to use effectively (though we hope not - the video above should help), but ImageJ plugin 2 should be very simple and useful to the broader community. I hope the community will appreciate our work. *3D visualize cells according to colocalization data *Export combined image series data to Matlab for 3D modeling Custom Matlab script: *Analyze and edit data from image series. *Import data from Colocalization Object Counter *Save data, load data, and export data to Excel. *Tools for subsequent 3D modeling/representation of data: draw tissue contours and indicate image-series global XY-origin. *Assign, classify and keep track of multichannel signal presence/absence (colocalization analysis) for each cell/object. *Quantity (count) cells/objects in a semi-automatic manner. ImageJ plugin 2: Colocalization Object Counter: ![]() Thicker 3D scans may be best to sub-divide into substacks (built-in ImageJ substack tool) prior to analysis with this tool. *Meant for tissue slices a few cell layers deep, depending on density of cells-of-interest. This simplifies the analysis of 3D colocalization data. ![]() *Can transform Z-stack 3D data into a specialized 2D Z-projection where Z-projection colocalization artifacts are removed/reduced. *Designed to help avoid common colocalization analysis artifacts and errors. *Pre-process multichannel Z-stack (or 2D) microscopy images into a visual format for faster, simpler, and more accurate colocalization analysis. Video explanation (Plugin 2 + Excel + Matlab): Features: ImageJ plugin 1: Colocalization Image Creator: Colocalization Object Counter An ImageJ plugin for cell-by-cell semi-automatic object based colocalization analysis
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |