Fiji plugin version of Pymagor. The functionality is much reduced compared to Pymagor. No trial alignment, averaging, report PDF, mat file export etc are available. Consider Pymagor for advanced analysis. This plugin will be useful for online analysis and you can take advantage of excellent Fiji plugins out there.
Feed a stack (i.e., calcium imaging time series) and get a frame average of raw pixel values for morphology and a dF/F response map (frame averaged). Optionally, you can get a dF/F movie (slow).
- Download Jymagor-master from "Download ZIP" button on the right or from https://github.com/i-namekawa/Jymagor/archive/master.zip
- Extract zip and rename the folder from "Jymagor-master" to "Jymagor"
- Copy the Jymagor folder to Fiji.app\plugins\Scripts
- Copy clut2b.lut in the Jymagor folder into luts folder (typically Fiji.app\luts)
- Fire up Fiji and Help -> Refresh Menus, Jymagor should be available under Main menu (reboot Fiji if not)
- Open a stack to analyze
- Find Jymagor menu (next to Help) and open the main panel (Jymagor -> Panel)
- Adjust the frame range for F (basal level) and Res (Response period)
- Click to activate the stack you want to analyze and press [Find target] button
- Press [Update] button on the main panel to get morphology and dF/F response map windows as well as Fiji's defaul ROI manager
- Daw and define ROIs on any of opened image windows and add them to the ROI manager
- Press [Plot] button on the main panel to get a plot of dF/F traces
- Save ROIs using ROI manager's interface