Skip to content

Commit

Permalink
Update release link
Browse files Browse the repository at this point in the history
  • Loading branch information
Trybuche committed Jun 2, 2021
1 parent 81d62d4 commit 14017c0
Showing 1 changed file with 13 additions and 10 deletions.
23 changes: 13 additions & 10 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -17,10 +17,10 @@ The "Draw Measurement" plugin then allows you to draw a line with the calibrated

## 🏗️ Installation
1. Download and install the [scientific image analysis program FIJI](http://fiji.sc)
1. Download the most recent [Microscope Tools Release from Github](https://github.com/elaniobro/Microscope-Measurement-Tools/releases)
1. Download the most recent [Microscope Tools Release from Github](https://github.com/Elaniobro/Microscope-Measurement-Tools/releases/tag/v2.4)
1. Extract/Unzip the file you downloaded from Github called: `Microscope-Measurment-tools`
1. Move the folder into the FIJI plugins directory on your MacOS
![](https://github.com/Elaniobro/Microscope-Measurement-Tools/blob/master/img/pkg_content.png)
<img src="https://github.com/Elaniobro/Microscope-Measurement-Tools/blob/master/img/pkg_contents.png?raw=true" width="600"/>



Expand All @@ -30,11 +30,11 @@ The "Draw Measurement" plugin then allows you to draw a line with the calibrated
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
![](https://github.com/Elaniobro/Microscope-Measurement-Tools/blob/master/img/roi.png)
1. Navigate to FIJI and select `Analyze > Set Scale`
<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
![](https://github.com/Elaniobro/Microscope-Measurement-Tools/blob/master/img/set_scale.png) mine is 5μm
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 @@ -64,10 +64,13 @@ The "Draw Measurement" plugin then allows you to draw a line with the calibrated
]
```
1. Quit FIJI
1. Re-start the FIJI application
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`.
![](https://github.com/Elaniobro/Microscope-Measurement-Tools/blob/master/img/microscope_calibrations.png?raw=true)
<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
Three files are included, which will show up in your FIJI "Analyze" menu:
Expand All @@ -76,11 +79,10 @@ Three files are included, which will show up in your FIJI "Analyze" menu:
+ *Opens the "Choose Calibration" window, for setting the measurement scale to a preconfigured value.*
+ **Draw_Measurement_-_Line.py**
+ *Converts a Line ROI into a drawn annotation with the measurement length indicated.*
+ **Microscope_Calibrations_user_settings.py**
+ *User-editable Settings file that contains your pre-configured scale calibrations, along with settings for drawing annotations (background/text color etc.)*
+ Please see the Instructions PDF for detailed instructions on setting up your settings file with Calibrations.
## 🔬 Microscope Calibration
View the [How-To Calibrate an Ocular Micrometer](https://www.youtube.com/watch?v=HaqgCtA-ioI&t=738s)
## 📐 Making + Drawing measurements
Expand All @@ -90,6 +92,7 @@ You can now drag a Line (or other type of ROI) on any feature, and the FIJI tool
To draw this measurement on your image, drag the Line to the desired location, and select the menu item `Plugins > Analyze > Microscope Measurement Tools > Draw Measurement - Line`
## 🔧 Custom Calibration Functions
A custom function can be added to the list of available calibrations (as opposed to a static scale value). A sub-folder is included showing an example of how to do this. The example is for a JEOL SEM (scanning electron microscope), and the example function will determine the scale of the SEM image by parsing an accompanying text file.
Expand Down

0 comments on commit 14017c0

Please sign in to comment.