hbakhtiar/AdaptFM_Testing

BBBC024

3D HL60 Cell line (synthetic data). This dataset contains a synthetic images of 3D cell nuclei. Images are stratified by clustering probability and SNR (low vs high). A complete description of the dataset can be found here

BBBC027

3D Colon tissue synthetic images. This dataset has synthentic images of 3D colon organoids. Images are stratified by low vs high SNR. A full description of the dataset can be found here

RESECT

Intraoperative brain tumor ultrasound images before, during, and after resection. Images are stratified by case (patient), with each case containing a before, during, and after resection ultrasound image. A complete description of the dataset can be found here

The dataset contains both original and ground-truth images.

ImageTBAD

CT scan image dataset of Type-B aortic dissection. The segmentation task involved segmenting true and false lumens, in addition to dissection thrombus. Note that not all images contain a thrombus. A full description of the dataset can be found here.

Organoids_Nuclear_Channel

A collection of nuclear-stained prostate cancer organoids. Manual annotations are provided, in addition to the manual counts of the number of nuclei (nuclear_true_counts.csv)

The first column of nuclear_true_counts.csv is the file name, and the second column is the number of distinct nuclei, as identified by a human annotator.

References

"We used image set BBBC024vl [Svoboda David, Kozubkek Michal, Stejskal Stanislav. Generation of Digital Phantoms of Cell Nuclei and Simulation of Image Formation in 3D Image Cytometry. Cytometry Part A, John Wiley & Sons, Inc., 75A, 6, pp. 494-509, 16 pages. ISSN 1552-4922. 2009.] from the Broad Bioimage Benchmark Collection."

"We used image set BBBC027 [Svoboda David, Homola Ondřej, Stejskal Stanislav. Generation of 3D Digital Phantoms of Colon Tissue, In International Conference on Image Analysis and Recognition - ICIAR 2011, Part II, LNCS 6754, Berlin, Heidelberg: Springer-Verlag, pp 31-39, June 2011] from the Broad Bioimage Benchmark Collection."

Yao, Z. et al. ImageTBAD: A 3D Computed Tomography Angiography Image Dataset for Automatic Segmentation of Type-B Aortic Dissection. Frontiers in Physiology Volume 12 - 2021 (2021). https://doi.org/10.3389/fphys.2021.732711

Xiao, Y., Fortin, M., Unsgård, G., Rivaz, H. & Reinertsen, I. REtroSpective Evaluation of Cerebral Tumors (RESECT): A clinical database of pre-operative MRI and intra-operative ultrasound in low-grade glioma surgeries. Medical Physics 44, 3875-3882 (2017). https://doi.org/https://doi.org/10.1002/mp.12268