Documentation on running the the 3D cell layer reconstruction tool, CellVolViewer.
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Obrain the latest release from
https://github.com/abiswas-odu/CellVolViewer/releases
. -
Unzip the file downloaded file and extract the release. Here we assume you are building in new subdirectory in your home directory:
mkdir ~/CellVolViewer
cd ~/CellVolViewer
tar -xvf ../CellVolViewer.tar.gz
Note the CellVolViewer tar file will be have a different name based on the version number.
- Let us assume that the unzipped path on the filesystem is PATH. This is the install path.
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Convert the z-stack of the image from the microscope into individual images in TIF or PNG format in Fiji.
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Each of those images should be converted into 8-bit greyscale images and saved in a folder with the z-stack index as the filename. For example, 1.tif, 2.tif ... .
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Each of the 8-bit greyscale images need to be segmented using CellViewer(see above) to generate the masks. This will produce a directory structure with a folder for each image and the handCorrected.tif mask inside it.
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Please see examples of the expected folder structure in the install path. For example "test_2".
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Now that the folder structure is setup. Let us assume it is called DATA. Create a text file inside DATA named config.txt. The config.txt contains various input parameters reqired to run the CellVolViewer commands. The expected parameters are described below. Please see an example of a config.txt inside the test folders.
// Image Pixel Dimensions
// x-axis in pixels
{x_px}
1024
// y-axis in pixels
{y_px}
1024
// number of z frames
{z_stack}
15
// number of interpolated frames in the 3D volume
{inprep_frames}
10
// Real Dimensions of the image in microns
{x_real}
176.68
{y_real}
176.68
{z_real}
15
// Placode area box. Dimemsion of a box that captures the placode cells only
{x_placode_min}
20
{x_placode_max}
1000
{y_placode_min}
20
{y_placode_max}
1000
Prerequisites: MATLAB > 2019b
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On MAC OSX you need to grant permission for the app to run. To grant permissions launch the
Terminal
app from Launchpad and execute the following commands:cd PATH chmod a+x gentracemap.exe
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Open the install folder PATH in MATLAB. In the MATLAB commandline run
gen_3d_vol DATA
. -
Run the command
gen_slice_view DATA
to look at the sliceView of the cells. The cells are tracked across the frames and the same cell across frames id colored the same. -
The cell tracking can be corrected by editing the
DATA\output\cell_tracks.csv
. The file has the same number of columns as the frames in the z-stack. The values are the cell IDs corresponding to the labels in the slice view. -
The masks can also be corrected to perform better 2D segmentation. Run
gen_slice_view DATA
again to show and label the new cells and assign them to tracks in cell_tracks.csv. -
After the cell tracking is complete, run
gen_cell_metrics DATA
to generate the final metics. a. It generates a file DATA\output\cell_areas.csv which has the cross section area of the cells in each frame and volumes. b. It generates a plot of the cross sectional area of each cell across each frame. -
To generate the 3D volume image of the cells, run
show_volume DATA
. It generates a 3D volume re-construction of the cells.