DOI: 10.6084/m9.figshare.23798451
title: ALFI dataset (final)

description: Data is divided into three folders: 1) Folder "Data&Annotations" includes images and annotations for all the sequences. 1.1) For sequences MI01 through MI08 (including annotations for both Task 1 and Task 2), the content is, e.g., ├── Data&Annotations │ ├── MI01 │ │ ├── Images │ │ │ ├── I_MI01_0001.png ... │ │ │ └── I_MI01_0069.png │ │ ├── MI01_DTLTruth.csv │ │ ├── MI01_PhenoTruth.csv │ │ └── Masks │ │ ├── M_MI01_0001.png ... │ │ └── M_MI01_0069.png For each j, I_MI01_j.png is the j-th image of video MI01 and M_MI01_j.png is the corresponding ground truth segmentation mask. The MI01_DTLTruth.csv file includes annotation information consisting of a) Number of sequence image (ImNo), b) Cell ID (ID), c) Cell class (Class, either Interphase or Mitosis), d) Bounding box, specified by its upper left corner (xmin, ymin) and its dimensions (width, height), and e) Parent cell ID (Parent). The MI01_PhenoTruth.csv file includes annotation information consisting of a) Number of sequence image (ImNo), b) Cell ID (ID), c) Cell class (Class, including EarlyMitosis, LateMitosis, CellDeath, and Multipolar), and d) Bounding box, specified by its upper left corner (xmin, ymin) and its dimensions (width, height). 1.2) For sequences CD01 through CD09 and TP01 through TP12 (including only annotations for Task 2), the content is similar, but there is no "Masks" subdirectory nor "*PhenoTruth.csv" file. 2) Folder "UseExamples" includes two usage examples and two directories including their output, in the form of Matlab/Python scripts. ├── UseExamples │ ├── UseExample1.m │ ├── UseExample1.py │ ├── UseExample1.py.readme.txt │ ├── UseExample1Out │ │ ├── TP06BBannots │ │ │ ├── TP06_py_WithBB_0001.png ... │ │ │ └── TP06_py_WithBB_0016.png │ │ │ ├── TP06_WithBB_0001.png ... │ │ │ └── TP06_WithBB_0016.png │ ├── UseExample2.m │ ├── UseExample2Out │ │ ├── MI01Lineage.png │ │ ├── MI01LineageCrops.png │ │ ├── MI02Lineage.png │ │ ├── MI02LineageCrops.png │ │ ├── MI03Lineage.png │ │ ├── MI03LineageCrops.png │ │ ├── MI04Lineage.png │ │ ├── MI04LineageCrops.png │ │ ├── MI05Lineage.png │ │ ├── MI05LineageCrops.png │ │ ├── MI06Lineage.png │ │ ├── MI06LineageCrops.png │ │ ├── MI07Lineage.png │ │ ├── MI07Lineage(Mitoses).png │ │ ├── MI07LineageCrops.png │ │ ├── MI08Lineage.png │ │ ├── MI08Lineage(Mitoses).png │ │ ├── MI08LineageCrops.png 2.1) UseExample1.m is a Matlab script for plotting the bounding box annotations over the original sequence images; the output is included in folder UseExample1Out/TP06BBannots, that contains images TP06_WithBB_0001.png, ..., TP06_WithBB_0016.png. UseExample1.py is the analogous examples written in Python and UseExample1.py.readme.txt is the related readme file; the output is included in folder UseExample1Out/TP06BBannots, that contains images TP06_py_WithBB_0001.png, ..., TP06_py_WithBB_0016.png. 2.2) UseExample2.m is a Matlab script for plotting the cells lineage for one of the sequences MI01-MI08; the output of this example is the lineage representation and image crops of mitotic cells given in the PNG images included in folder UseExample2Out. For the user convenience, we provide the output images for all MI* sequences, without need to run it. Please, observe that, for the very crowded sequences MI07 and MI08, we also also provide the lineage representation reduced only to Mitoses (e.g., MI07Lineage(Mitoses).png), obtained setting the parameter OnlyMitoses = 1; (line 49 of the script). 3) Folder "Videos" includes the 29 videos stored in ND2 format. └── Videos ├── CD01.nd2 ... └── TP10.nd2