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Fix list numbers
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I did not realize that images have to be part of a list item or it breaks the list.
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Elaniobro authored Jun 13, 2021
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Expand Up @@ -29,12 +29,10 @@ The "Draw Measurement" plugin then allows you to draw a line with the calibrated
1. Open FIJI
1. Open an image file taken at the desired maginification with a measurment marker. e.g. Open a photo of your micrometer slide taken with your 40x objective
1. Zoom in on the photo to view the micrometer scale
1. Draw a line `ROI` (Region Of Interest) along the calibration measurment feature. e.g. along the micrometer
<img src="https://github.com/Elaniobro/Microscope-Measurement-Tools/blob/master/img/roi.png?raw=true" width="600"/>
1. Draw a line `ROI` (Region Of Interest) along the calibration measurment feature. e.g. along the micrometer <img src="https://github.com/Elaniobro/Microscope-Measurement-Tools/blob/master/img/roi.png?raw=true" width="600"/>
1. Navigate to and select `Analyze > Set Scale`
1. The "Distance in Pixels" will already be set by your line ROI
1. Type in the "Known Distance" from your measurement feature, mine is 5μm
<img src="https://github.com/Elaniobro/Microscope-Measurement-Tools/blob/master/img/set_scale.png?raw=true" width="600"/>
1. Type in the "Known Distance" from your measurement feature, mine is 5μm <img src="https://github.com/Elaniobro/Microscope-Measurement-Tools/blob/master/img/set_scale.png?raw=true" width="600"/>
1. Record the resulting "Scale" value, e.g. 31.1716 pixel/unit, where unit is cm, mm, μm, etc
1. The "Scale" value will be used in your `Microscope_Calibrations_user_settings.py` file, so recored both a name and the scale value. e.g:
```
Expand Down Expand Up @@ -67,9 +65,8 @@ The "Draw Measurement" plugin then allows you to draw a line with the calibrated
1. Re-start the FIJI application. This will allow the application to register the changes you made to the plugin
**note** _for any subsquent changes, you will have to save the file, quit the application and re-open it to see the changes_
1. Open an image
1. Run `Analyze > Microscope Measurment Tools > Choose Microscope Calibration` and see a pop-up window that shows the new names and calibration values you set in `Microscope_Calibrations_user_settings.py`.
<img src="https://raw.githubusercontent.com/Elaniobro/Microscope-Measurement-Tools/master/img/microscope_calibrations.png" width="600"/>
1. You may also apply the same scale and scale bar to all images you have open, but selecting the checkboxes. Doing so will open another pop-up, where you can see how the scale will look. In the example below, the bar is set to 10μm, white text and placed in the lower right corner
1. Run `Analyze > Microscope Measurment Tools > Choose Microscope Calibration` and see a pop-up window that shows the new names and calibration values you set in `Microscope_Calibrations_user_settings.py`. <img src="https://raw.githubusercontent.com/Elaniobro/Microscope-Measurement-Tools/master/img/microscope_calibrations.png" width="600"/>
1. You may also apply the same scale and scale bar to all images you have open, but selecting the checkboxes. Doing so will open another pop-up, where you can see how the scale will look. In the example below, the bar is set to 10μm, white text and placed in the lower right corner
<img src="https://raw.githubusercontent.com/Elaniobro/Microscope-Measurement-Tools/master/img/scale_bar.png" width="600"/>
## 📈 Usage
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