Example dataset to test MitoGraph on and ImageJ macros to help you to prepare your data.
Matheus Viana - [email protected] - 01.19.2018
Click here to download our example dataset and ImageJ macros. We recommend you to unzip the file in your Desktop.
We made availabe five images of mitochondria in budding yeast cells grown in glucose. These cells have been imaged in a spinning disk confocal microscope and their pixel size is 0.056x0.056x0.200µm. To execute MitoGraph type the following command in the terminal of your Mac OS (spotlight + terminal):
cd ~/Desktop/MitoGraph
./MitoGraph -xy 0.056 -z 0.2 -path ~/Desktop/MitoGraphTools-1.0
Inspecting the output files filename.mitograph you should get these values:
| File | Volume from voxels (µm3) | Average width (µm) | Std width (µm) | Total length (µm) | Volume from length (µm3) |
|---|---|---|---|---|---|
| BuddingYeastGlucose01 | 4.23674 | 0.22246 | 0.03501 | 46.57995 | 3.29254 |
| BuddingYeastGlucose02 | 5.23900 | 0.22189 | 0.03842 | 55.27222 | 3.90696 |
| BuddingYeastGlucose03 | 2.03777 | 0.24329 | 0.03732 | 15.97084 | 1.12891 |
| BuddingYeastGlucose04 | 2.54079 | 0.24168 | 0.03439 | 23.62560 | 1.67000 |
| BuddingYeastGlucose05 | 2.01331 | 0.23770 | 0.04171 | 16.01066 | 1.13173 |
Each of these images is processed in ~25s in a MacBook Pro 2,9 GHz Intel Core i7.
MitoGraph performs better over single cell images similar to the images from our test dataset. Here we provide two ImageJ macros that helps you to format your images in that way. If you have any questions about how to use these macros, please contact us.
This macro is used to generate a z-stack where each slice corresponds to the max projection of a z-stack. The z-stack generated here is used to draw ROIs around the cells you want to analyze individually with MitoGraph.
Warning: make sure your files names are shorter than 60 characters and do not contain empty spaces. A common practice is to replace empty spaces with underscore (_).
USING THIS MACRO:
- Click run to execute the macro
- Select the folder that contains the original z-stacks
- A file named MaxProjs.tif will be created inside the chosen folder
This macro is used to create single cells z-stacks similar to the one available in the example dataset.
BEFORE USING THIS MACRO:
- Use the macro GenFramesMaxProjs.ijm to generate the z-stack MaxProjs.tif
- Use the z-stack MaxProjs.tiff to drawn ROIs around the cells that you want to crop
- Save the ROIs as RoiSet.zip
USING THIS MACRO:
- Click run to execute the macro
- Select the size of the single cell images you want to create. The default value should be fine for images of mitochondria of yeast cells. You may want to increase this value if your cells are bigger (e.g. mammalian cells)
- Select the folder that contains the original z-stacks, the file RoiSet.zip and the file MaxProjs.tiff
- A subfolder called cells will be created and should be used as input for MitoGraph