Cell Plotcontains only one single .exefile, and doesn’t require installation. It also doesn’t rely on any external software bundles, like MATLABor Javavirtual machine. Cell Plothas a built-in color mixer, allowing users to change channels to display.
- User can select cells to be included in the final results – simply double click a cell to include/exclude it.
- Cell boundary can be modified by moving the boundary points. Clicking on the lines adds end points. Double clicking on a point removes it.
- Holding the
Altkey and draw a shape around a nucleus, the cell boundary will be replaced with the shape.
- Direction of cell migration (the arrow) can be changed by moving the arrow. The arrow is used as the Y-axis of the cell in all measurements.
- Centrosome position (white dot) can be moved.
- All images in an experiment can be saved as stacks and can be analyzed at the same time. Use
PgUpand PgDnto navigate between images.
- Final results can be copied to the clipboard. Simply paste them in to
Excelfor further statistical analysis.
- All results, including manually changed cell boundaries, are automatically saved (in a file named
CellPlot.dat), so that a user can always go back and review/modify their analysis. Note: a single CellPlot.datis created in a folder, and is used for all images in that folder.
- A data inspector provides real time summary of the results. Top of the inspector is a plot, in which each point represents result from a cell. Clicking on a point moves to the image with the cell and highlights the cell.
Cell Plotcan open regular .tiffiles and .stkfiles (a TIFF variant used by Metamorph). TIFF files with a single image or a stack of images are supported. When using images with single channel, the file name should ended with -G, -R, -B, -I, -Green, -Red, -Blue, or -FarRed(case-insensitive). When opening a file whose name ended with them, Cell Plotwill look for the other files and open them as a multi-channel image. Cell Plotcan open old .lsmfiles from Zeiss microscopes. Cell Plotcan open new .czifiles from Zeiss microscopes.
- Nikon considers the ND2 file format private and will not publish its specification.
Cell Plotcan open .nd2files from Nikon microscopes, but it requires the installation of a DLL library from Nikon’s SDK. Please request the SDK from Nikon and extract its DLL files in to a subfolder named Nd2Readernext to CellPlot.exe. It may not work though, as my experiences with the DLL library varied, especially on Windows 10.
How to use
- Double click to run
- Drag and drop one of the
.stkfiles to on Cell Plot.
- Click the “Cell” button and
Cell Plotwill start to analyse the images.
- Use the mouse to play around with the boudaries, the centrosome dots and the arrows.
- Have fun!
Here is a short close-captioned video tutorial.