MetaXpress Software: Analysis Training
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1 MetaXpress Software: Analysis Training
2 MetaXpress: Application Modules Canned, walk-away automation Advanced segmentation, feature detection, and measurement Site-by-site and cell-by-cell data Validated results Can be incorporated into a journal for increased customization
3
4 MetaXpress: Application Modules All Application Modules share the same basic controls Simple configuration Select wavelength Set size range of objects Set intensity above local background Test and save settings The module will automatically split touching cells
5 Adaptive Background Correction Built in background management Adaptive Background Correction is automatically performed by each application module Detection even in noisy and poorly stained images Splits touching cells Consistent performance across multiple plates
6 Configuring settings the basics
7 Optimizing settings Only change one parameter at a time Min width has the most drastic effect
8 Measuring width Use the line tool Measure across the short axis Find a small cell and a large cell
9 Measuring Intensity above Local Background 1. Find a dim cell 2. Measure intensity just inside and outside the cell 3. Subtract to find the difference ( = 786) 4. Pad the value by about 100 gray values ( = 686). Note: For FAST algorithm, cut this value in half.
10 Selecting measurements Summary log = Site by Site data Total cells, intensity, average area, etc.
11 Selecting measurements Data log = Cell by cell data Area, intensity, etc. for each individual cell
12 Selecting measurements Configure Summary Log Configure Data Log
13 MetaXpress - Interactive Analysis Optimization Module interactive feedback Interactive optimization of analysis parameters Immediate graphic feedback on detection results Links numerical results to image overlays
14 Logging out your data Four types of logs in MetaXpress Data Log: Opens an existing or new data log for storing measurements other than morphometric measurements Summary Log: Opens an existing or new summary log for storing summaries of morphometry statistics Object Log: Opens an existing or new object log for storing per-object morphometric measurement data Edge List Log: Opens an existing or new edgelist log for storing each object's centroid and vertex X,Y-coordinate data in an image Log to a text file or to Microsoft Excel using DDE (Dynamic Data Exchange)
15 Opening and closing logs Log menu Open Close Pause / Resume (useful in journals)
16 Opening and closing logs Log menu Open Close Pause / Resume (useful in journals) Specific measurement dialogs Open Log button turns into Log Data
17 Opening and closing logs Log menu Open Close Pause / Resume (useful in journals) Specific measurement dialogs Open Log button turns into Log Data For MS Excel, select Dynamic Data Exchange Specify sheet name If sheet not open, new sheet will be created in currently open workbook If no workbook open, new one will be created
18 Screening > Review Plate Data Select plate for review
19 Select plate for review Configure branches
20 Review Plate Data: Display Tab Data view Wavelength selection Configure thumbnail montage area Color overlay option
21 Review Plate Data: Run Analysis Tab Create Custom Module appears if you have the Custom Module Editor option on key. Options missing <> are custom assays.
22 Review Plate Data: Run Analysis Tab Configure module settings Run analysis for all positions, a subset of marked selections, or current image displayed. Right click on wells to mark as selection. Turn off heat map to see marked selections (in green).
23 Review Plate Data: Measurements Tab Select analysis & measurement parameter to view in data table
24 Review Plate Data: Measurements Tab Show heat map. Toggle on/off.
25 Review Analysis Results Within MetaXpress
26 Review Plate Data: Graph Tab
27 Screening > Plate Data Utilities
28 Screening > Plate Data Utilities > Export Measurements
29 Plate Data Utilities: Run Analysis for Batch Analysis
30 Add Analysis to Database: Custom Analyses Assay will appear in Run Analysis tab. Add Analysis to Database is only used if you create your own custom analysis with a journal (macro).
31 Add Analysis to Database: Custom Module Custom Module will appear in Run Analysis tab.
32
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