Supported image formats

The program was made with movies of grayscale 3D images in mind. Multiple channels (for example captured at different wavelengths) are supported.

There is some basic support for 2D images. They will be loaded as 3D images with only a single xy plane.
If you try to load a colored image (like a PNG file), then the image will be converted to grayscale.

LIF, CZI and ND2 files

LIF files are used by Leica microscopes, CZI files by Zeiss microscopes and ND2 files by Nikon microscopes. All of these file types contain images of all available time points in a single file. To load a file, simply select File -> Load images... and select the file. If your file contains multiple time series, you will be prompted to pick one.

IMS files

IMS files are used by Imaris. OrganoidTracker only has basic support for those files: it will read the images, but not anything else, like segmentation or tracking data. To load an Imaris file, simply select File -> Load images... and select the file.

A folder containing one 3D image for every time point

Many biologists save images like image_0.tif, image_1.tif, image_2.tif etc., with each image representing a single channel of a single time point. If you load an image from time point 0 or 1, the program will automatically try to search for other images with a similar naming pattern. The program is able to recognize the following naming patterns:

Images ending with a number, like image0.png, image1.png, image2.png. The number will be interpreted as a time point number. (Brackets) around the number are allowed.
Images containing the letter t followed by a number, like nd56t1.tif, nd56t2.tif. The number will be interpreted as a time point number. A captial T instead of a t is also allowed.
Images containing the letter c followed by a number, like nd56t1c1.tif, nd56t1c2.tif. The number will now be interpreted as a channel. A capital C instead of a c is also allowed.

Leading zeroes (like in image_0001.png) are supported.

A multi-page TIFF file

If instead only a single TIFF file is found, OrganoidTracker assumes that an the entire time-series is saved to that file. OrganoidTracker uses the tifffile Python package to read the metadata of the file, to found our how the file is constructed. If OrganoidTracker doesn’t understand the file format, an error message is displayed.

A single image

If the program cannot find any pattern in the file name, and the file is not a multi-page TIFF file, it will display a warning and load only that image. You’ll end up with a “movie” of only one time point.