https://github.com/JaneliaSciComp/ColorMIP_Mask_Search
ColorMIP_Mask_Search plugin for Fiji
https://github.com/JaneliaSciComp/ColorMIP_Mask_Search
Last synced: about 2 months ago
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ColorMIP_Mask_Search plugin for Fiji
- Host: GitHub
- URL: https://github.com/JaneliaSciComp/ColorMIP_Mask_Search
- Owner: JaneliaSciComp
- Created: 2018-02-21T18:06:33.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2023-11-08T20:36:21.000Z (over 1 year ago)
- Last Synced: 2024-04-07T01:49:28.191Z (about 1 year ago)
- Language: ImageJ Macro
- Size: 53.3 MB
- Stars: 4
- Watchers: 6
- Forks: 12
- Open Issues: 6
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Metadata Files:
- Readme: README.md
Awesome Lists containing this project
- awesome-janelia-software - ColorMIP Mask Search - Fiji plugin for color depth search (Fiji Plugins)
- awesome-janelia-software - ColorMIP Mask Search - Fiji plugin for color depth search (Fiji Plugins)
README
# Color-MIP Mask Search [](https://www.janelia.org)
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).
***For EM MIP search please use this EM search [plugin](https://github.com/JaneliaSciComp/EM_MIP_search)
***Downloading the Color Depth MIPs are [here](https://open.quiltdata.com/b/janelia-flylight-color-depth/tree/Color_Depth_MIPs_For_Download/)
***The unisex brain template for the CDM resolution can be found [here](https://open.quiltdata.com/b/janelia-flylight-color-depth/tree/alignment_templates/JRC2018_UNISEX_20x_HR.nrrd)
## Before starting
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](https://github.com/JaneliaSciComp/ColorMIP_Mask_Search/blob/master/Color_MIP_Mask_Search.jar))
## Startup
Drag the folder (containing Gal4 color depth MIPs) into fiji, use virtual stack option.
## Create mask of neuron of interest
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.
## Search stacks with mask
Plugins > ColorMIP Mask search
### considerations/ tips:
- 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.
## Synchronize windows
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.
## Create a list of candidate lines
`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.
## Demo movie
[](https://youtu.be/JVZs19yvEqY)