| DSB2018 |
(~300, ~300) |
1, 3 |
735 (670/65) |
uint8 |
PNG |
● (I) |
Kaggle; Mixture of images here and there; Also known as BBBC038 |
Data Science Bowl 2018 |
[DSB2018](https://www.kaggle.com/c/data-science-bowl-2018) |
| 
|
| StarDist |
(~300, ~300) |
1, |
497 (447/50) |
uint8 |
TIF |
● (I) |
For StarDist model; Subset of DSB2018; All grayscale |
StarDist - Object Detection with Star-convex Shapes |
[StarDist](https://github.com/stardist/stardist/releases/download/0.1.0/dsb2018.zip) |
| 
|
| ComPath |
(1000, 1000) |
3 |
30 |
uint8 |
PNG |
● (I) |
H&E; Instance segmented; dense |
A Dataset and a Technique for Generalized Nuclear Segmentation for Computational Pathology |
[IEEE Xplore](https://ieeexplore.ieee.org/document/7872382) |
| 
|
| FRUNet |
(2048, 2048) |
1 |
72 |
uint16 |
TIF |
● (I) |
TEM images |
FRU-Net: Robust Segmentation of Small Extracellular Vesicles |
[Nature](https://www.nature.com/articles/s41598-019-49431-3) |
| 
|
| S_BSST265 |
(430, 550) - (1024, 1360) |
1, 3 |
79 (42/37) |
uint8 |
TIF |
● (I) |
IF images; Designed for ML |
An annotated fluorescence image dataset for training nuclear segmentation methods |
[Nature](https://www.nature.com/articles/s41597-020-00608-w) |
| 
|
| BBBC006 |
(520, 696) |
2 |
768 |
uint16 |
TIF |
● (I) |
Have z-stack; z=16 is in-focus ones; sites (s1, s2); w1=Hoechst, w2=phalloidin |
Human U2OS cells (out of focus) |
[BBBC006](https://bbbc.broadinstitute.org/BBBC006) |
| 
|
| BBBC020 |
(1040, 1388) |
2 |
25 |
uint8 |
TIF |
● (I) |
Cell & Nuclei anno; 5 missing annotations |
Murine bone-marrow derived macrophages |
[BBBC020](https://bbbc.broadinstitute.org/BBBC020) |
| 
|
| BBBC039 |
(520, 696) |
1 |
200 |
uint16 |
PNG |
● (I) |
Samples from BBBC022; Annotated; May have some overlap with DSB2018 |
Nuclei of U2OS cells in a chemical screen |
[BBBC039](https://bbbc.broadinstitute.org/BBBC039) |
| 
|
| Cellpose |
(~383, ~512) |
3 |
608 (540/68) |
uint8 |
PNG |
● (I) |
For Cellpose model; Various sources, not only bioimages |
Cellpose: a generalist algorithm for cellular segmentation |
[Cellpose](https://www.cellpose.org/dataset) |
| 
|
| LIVECell |
(520, 704) |
3 |
5239 |
int32 |
TIF |
● (I) |
HUGE dataset (3727 train, 1512 test); 3 channels (R, G, B) |
LIVECell dataset |
[LIVECell](https://www.nature.com/articles/s41592-021-01249-6) |
| 
|
| TNBC |
(512, 512) |
3 |
50 |
uint8 |
PNG |
● (F) |
H&E; Triple Negative Breast Cancer |
Segmentation of Nuclei in Histopathology Images by Deep Regression of the Distance Map |
[IEEE Xplore](https://ieeexplore.ieee.org/document/8438559) |
| 
|
| BBBC004 |
(950, 950) |
3 |
100 |
uint8 |
TIF |
● (F) |
3 channels (R, G, B) |
Synthetic cells |
[BBBC004](https://bbbc.broadinstitute.org/BBBC004) |
| 
|
| BBBC008 |
(512, 512) |
2 |
12 |
uint8 |
TIF |
● (F) |
F/B semantic segmentation |
Human HT29 colon-cancer cells |
[BBBC008](https://bbbc.broadinstitute.org/BBBC008) |
| 
|
| MurphyLab |
(1024, 1344), (1030, 1349) |
1 |
100 |
uint8 |
PNG |
● (O) |
Two annotation formats; Photoshop and GIMP; 97 segmented images |
Nuclei Segmentation In Microscope Cell Images: A Hand-Segmented Dataset And Comparison Of Algorithms |
[MurphyLab](http://murphylab.web.cmu.edu/data/2009_ISBI_Nuclei.html) |
| 
|
| BBBC007 |
(400, 400) - (512, 512) |
2 |
16 |
uint8 |
TIF |
● (O) |
Outline annotation |
Drosophila Kc167 cells |
[BBBC007](https://bbbc.broadinstitute.org/BBBC007) |
| 
|
| BBBC009 |
(600, 800) |
3 |
5 |
uint8 |
TIF |
● (O) |
DIC images; 3 channels (R, G, B) |
Human red blood cells |
[BBBC009](https://bbbc.broadinstitute.org/BBBC009) |
| 
|
| BBBC018 |
(512, 512) |
3 |
56 |
uint8 |
DIB |
● (O) |
Outline anno; One missing annotation (ind=55) |
Human HT29 colon-cancer cells (diverse phenotypes) |
[BBBC018](https://bbbc.broadinstitute.org/BBBC018) |
| 
|
| BBBC030 |
(1032, 1376) |
3 |
60 |
uint8 |
TIF |
● (O) |
DIC images; 3 channels (R, G, B) |
Chinese Hamster Ovary Cells |
[BBBC030](https://bbbc.broadinstitute.org/BBBC030) |
| 
|
| BBBC041 |
(1200, 1600), (1383, 1944) |
3 |
1,328 (1,208/120) |
uint8 |
PNG, JPEG |
● (U) |
Bounding box; Not 1368 images as described in BBBC?; RGB and YUV space |
P. vivax (malaria) infected human blood smears |
[BBBC041](https://bbbc.broadinstitute.org/BBBC041) |
|
| DigitPath |
(2000, 2000) |
3 |
141 |
uint8 |
TIF |
▲ (F) |
H&E; partially annotated |
Deep learning for digital pathology image analysis: A comprehensive tutorial with selected use cases |
[PubMed Central](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4977982/) |
| 
|
| UCSB |
(768, 897) |
3 |
58 |
uint8 |
TIF |
▲ (F) |
H&E; partially annotated; Two categories (benign, malignant) |
A biosegmentation benchmark for evaluation of bioimage analysis methods |
[PubMed Central](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2777895/) |
| 
|
| BBBC002 |
(512, 512) |
1 |
50 |
uint8 |
TIF |
X (C) |
May overlap with DSB2018 |
Drosophila Kc167 cells |
[BBBC002](https://bbbc.broadinstitute.org/BBBC002) |
|
| BBBC013 |
(640, 640) |
2 |
96 |
uint8 or uint16 |
BMP or FRM |
X (B) |
Cytoplasm |
Human U2OS cells cytoplasm–nucleus translocation |
[BBBC013](https://bbbc.broadinstitute.org/BBBC013) |
|
| BBBC014 |
(1024, 1360) |
2 |
96 |
uint8 |
BMP |
X (B) |
Second channel is usually very clear with a few artifacts |
Human U2OS cells cytoplasm–nucleus translocation |
[BBBC014](https://bbbc.broadinstitute.org/BBBC014) |
|
| BBBC015 |
(768, 1000) |
2 |
144 |
uint8 |
JPEG |
X (B) |
2 channels (Green, Crimson); Texture in green channel |
Human U2OS cells transfluor |
[BBBC015](https://bbbc.broadinstitute.org/BBBC015) |
|
| BBBC016 |
(512, 512) |
2 |
72 |
uint8 |
TIF |
X (B) |
2 channels (G,B); Cells are Blue |
Human U2OS cells transfluor |
[BBBC016](https://bbbc.broadinstitute.org/BBBC016) |
|
| BBBC026 |
(1040, 1392) |
1 |
864 |
uint8 |
PNG |
X (B, C) |
Only centers are annotated for 5 imgages |
Human Hepatocyte and Murine Fibroblast cells – Co-culture experiment |
[BBBC026](https://bbbc.broadinstitute.org/BBBC026) |
|
| BBBC021 |
(1024, 1280) |
3 |
132,000 |
uint16 |
TIF |
X (B) |
HUGE dataset; 3 channels; DAPI(w1), Tubulin(w2), Actin(w4) |
Human MCF7 cells – compound-profiling experiment |
[BBBC021](https://bbbc.broadinstitute.org/BBBC021) |
|