The algorithm created by Hideo Otsuna.
FIJI plugins created by Hideo Otsuna and Takashi Kawase.
This manual is modified based on the instruction developed by Justine X Chia (UCSF).

1. Launch and update FIJI.
2. Drag and drop ColorMIP_Mask_Search.jar on FIJI then quit (the plugin installation).
   (you can get the .jar file from here)

Drag the folder (containing Gal4 color depth MIPs) into fiji, use virtual stack option.

1. Duplicate a single slice that containing the neuron from the Gal4 image (⌘⇧ D).
2. Trace area of interest on a duplicated slice (use polygon tool and try to be as accurate as possible).
3. Edit > Clear Outside.

Plugins > ColorMIP Mask search

• Show log // -> show NaN for log may be useful for a first pass, just to keep track of all slices.
• Threshold for data: 30-60 is a good place to start for searching Gal4.
• If background is too high, increase threshold (max value is 255).
• If too many hits, can try increasing % of Positive PX Threshold 5-10%.
• The search can stop by pushing escape.

To make sure the position between the mask (the neuron) and hits (Gal4 lines), synchronizing the wingdows is useful function.

1. Analyze > Tools > Synchronize Windows.
2. Select the two windows to synchronize.

A red x (cross-hair) will now appear at the same position in both images.

realtime_Result_ctrl_click_substack.ijm is useful for quickly making a list of lines and the substack while scrolling through the stack of potential hits.

1. Open realtime_Result_ctrl_click_substack.ijm.
2. Click window with colorMIP search result stacks.
3. Run macro (only accepts one open window). Then Result window will be open.
4. Shift + click on the result stack will add the image name into the Result table.
5. ctrl + click will create a substack with the Result table from the result stack.