mibi_tsai

The Tile/SED/Array Interface (TSAI) is a tool for rapidly setting up FOVs on the Ionpath Multiplexed Ion Beam Imaging (MIBI) microscope (MIBIscope). This branch updates MIBI TSAI for the new MIBIcontrol v1.8 software but is backwards-compatible.

Table of Contents

• 1. Online version
• 2. Local installation
• 3. Usage instructions
• 4. Updates

1. Online version

The easiest way to use this tool is to open the working, online version at https://tsai.stanford.edu/research/mibi_tsai on your MIBIscope computer. However, it contains presets which may not apply across all instruments. Thus, when using it you should only build from FOVs exported from your specific instrument's MIBIcontrol.

2. Local installation

If you wish to integrate your instrument's FOV presets as well as links to your MIBItracker and run log, you may set up your own version on any web host. There are no server-side commands, thus no access to PHP, Python, SQL, etc. is required.

1. Use MIBIcontrol to create a .json file containing all your preset imaging modes and dwell times.
2. Download mibi_tsai_standalone to a new folder. Within the _resources subfolder, open index.js in any text editor.
3. Edit tsai.url_run_log(''); to include your run log, e.g. tsai.url_run_log('https://docs.google.com/spreadsheets/d/...');.
4. Edit tsai.url_mibi_tracker(''); to include your MIBItracker address, e.g. tsai.url_mibi_tracker('https://your_lab.ionpath.com');.
5. For each line tsai.dwell_add('# ms', #);, edit the dwell times and timing choices to match those in your .json file.
6. For each line tsai.preset_add('...', {...});, edit the preset names and FOV JSONs to match those in your .json file.
7. For each line tsai.preset_recommended('...', [...]);, edit the preset/dwell time combinations to match those recommended on your MIBIcontrol.
8. Uncomment (remove // from) and edit the various other presets to change the default style settings, e.g. line thickness or arrow key nudge distance.
9. Save your changes to index.js.
10. Upload mibi_tsai_standalone to the web server and perform chmod 755 *.* on all directories.
11. Open index.html.

3. Usage instructions

Screen capture videos will be submitted as part of a manuscript submission. Usage instructions will also be placed on on protocols.io if accepted.

4. Updates

Changes from the prior branch include:

1. Accommodating in-run autofocus (Walkaway Mode) with addition of focusSite and focusOnly parameters. FOVs are grouped by closest autofocus point and a toggle control is added for drawing 5mm radius circles around focus sites.
2. Tiles are labeled on the slide image by default, but labels can be toggled off. Saving the tiled image will include the labels (if present) into the PNG file. This is especially convenient for documentation and sending to collaborators.
3. Keyboard controls are added for the slide image options, including (Z)oom, (B)rightness, and (C)ontrast.
4. JSON output control options (FOV grouping, resume, split) are simplified and JSON build/download buttons generated dynamically as soon as options are changed.
5. A section is added to rearrange FOVs, mainly for in-run Molybdenum Foil points.
6. Error-checking updates: A. Additional checks for focus sites, B. Slide boundary units in index.js are now in decimals rather than pixels to account for optical image zooming.
7. Tiled SED scanning now moves horizontally before vertically, found on limited testing to be slightly more accurate than vertically before horizontally.
8. Many other small interface enhancements, code simplifications, and bug fixes.