This is a mirror of the the inner README file of the full dataset describing naming conventions and data format.
The data formatting conventions are also applicable to the non compressed sample data presented in the folder "170314_Clb2Mad2_Cdc20MultipleCopie_washout/"
The data presented in the folder Others is not annotated

--- full_yeast_dataset.zip inner readme ---

This folder structure contains raw microscopic recordings of yeast cells in .TIFF format (movies folders), and their manually curated ground-truth annotation in .TXT formats (contours folders) for both training and test sets used in our publication "Enhancing Yeast Cell Tracking with a Time-Symmetric Deep Learning Approach".

The .TIFF format recordings contain phase-contrast and fluorescent channels periodically, from which only the phase-contrast channels were used both during training and evaluation. These can be processed similarly to the example presented in https://github.com/SzaboGergely0419/PPCU_IFOM_YeastTracker, and the utilized function "LoadVideoFromSingleTIFF" defined in https://github.com/SzaboGergely0419/PPCU_IFOM_YeastTracker/blob/main/ppcu_ifom_yeasttracker/general_functionalities/video_loading.py.

The .TXT annotations contain tracking and polygonal instance segmentation (no postfix) and inheritance ("_mothers" postfix) informations in the train set, and only tracking information in the test set. Furthermore, in the train set, for the tracking annotation the position of the microfluidic well is denoted as POS, while in the test set it was removed for easier compliance with the prediction format.

The other, more important columns of the tracking annotation format are as follows:
- F: Frame of the polygon vertex coordinate
- CELLNUM: ID of the given track (not the object instance, but F and CELLNUM uniquely identifies an object instance)
- X, Y: The polygon vertex coordinate
It is always expected that the polygons are closed loops, the loading of such file formats should be performed like in the example presented in https://github.com/SzaboGergely0419/PPCU_IFOM_YeastTracker, and the utilized function "LoadAnnotation" defined in https://github.com/SzaboGergely0419/PPCU_IFOM_YeastTracker/blob/main/ppcu_ifom_yeasttracker/tracking/tracker_utilities.py.

While the inheritance data was not utilized for the publication, it is also manually curated and usable for evaluation purposes.
Its column are as follows:
- pos: Position in the microfluidic well, compatible with POS
- CellNum: ID of the given mother track (not necessarily unique as a single cell can have multiple offsprings), compatible with CELLNUM
- DaughNum: ID of the given daughter track (unique, as one cell should only have a single mother), compatible with CELLNUM
- BirthFrame: The first frame on which the daughter cell was detected, compatible with F

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