Cochlea_Tools

Measure the area of the cochlea, the dead cells, the dead cells inside the cochlea and the length of the cochlea.

The source code in github can be found here.

Getting Started

You need to have the MorpholibJ plugin installed.

To install the tool save the file cochlea_tools.ijm into the folder macros/toolsets of your FIJI installation.

Select the "cochlea_tools" toolset from the >> button of the ImageJ launcher.

Cochlea tools help (f4)

Open this help page.

Measure Area of dead cells (f5)

Threshold the dead cells channel to measure the area of dead cells relative to the image area.

Measure area of cochlea (f6)

Threshold the cochlea channel to measure the area of cochlea relative to the image area.

Measure length of cochlea (f7)

Measure the length of the cochlea in the first slice of the image.

Measure area of dead cells in cochlea (f8)

Calculate and measure the intersection between dead cells and the cochlea.

Analyze image (f9)

Run all the before mentioned steps on the image.

Batch analyze images (f10)

Run all the before mentioned steps on all tif files in a folder. Save the images with the overlay and a file containing the measures.

Usage

A right click on one of the buttons opens the options dialog. The options dialog allows to specify which channels contain the cochlea and the dead cells, to change the thresholding methods used, to modify what is considered as part of the cochlea and how much to smooth the length calculation.

You can use the buttons from left to right to run the consecutive steps, or you can use the a-button to run all steps automatically. You can also use the b-button to run all steps on all images inside a folder.

Options

Right-click on any of the buttons to open the options-dialog.

dead cells channel

The channel containing the dead cells

dead cells thresholding method:

The thresolding method used to find the dead cells.

cochlea channel:

The channel containing the cochlea.

cochlea thresholding method:

The thresolding method used to find the cochlea.

close count:

Amount of smoothing of the cochlea found, increase this parameter if some parts that should be connected are separated.

cochlea size threshold:

The minimal area that must be detected so that the selection is considered part of the cochlea, increase this parameter if unwanted elements are considered as part of the cochlea or reduce it if small parts of the cochlea are left out.

interpolation length:

The amount of smoothing done on the cochlea length measurement.

Notes

• Output of the batch will be written into a output-folder.
• Measures obtained with the batch will be saved in output/Batch Cochlea Results.csv
• It's possible to make a selection to reduce the area of the analysis.