Downloads#
Note
Rows with an entry in the Segmentation/Spots column mean that download contains the pre-computed segmentation labels and/or spot detection coordinates for that dataset.
Course Data#
03 - Introduction to Digital Images
| Item | Dataset | Segmentation/Spots | Notes |
|---|---|---|---|
| Working with Bioimages | Working with Bioimages Dataset | – | – |
04 - Image Segmentation
| Item | Dataset | Segmentation/Spots | Notes |
|---|---|---|---|
| Classical Methods | Segmentation and Spot Detection Dataset | Segmentation and Spot Detection Results | Generated from CCDB_6843 |
| Machine Learning Methods - Ilastik Pixel Classification | Ilastik Pixel Classification Dataset | Ilastik Pixel Classification Results | From Ilastik Data Mitocheck 2D+t |
| Deep Learning Methods - Cellpose | Segmentation and Spot Detection Dataset | Segmentation and Spot Detection Results | Same dataset as `Classical Methods`, generated from CCDB_6843 |
| Deep Learning Methods - Cellpose 3D | Cellpose 3D Dataset | – | From BBBC033 |
| Deep Learning Methods - Cellpose Training Dataset | Cellpose Training Dataset | – | From Cellpose Github Repository |
05 - Spot Detection
| Item | Dataset | Segmentation/Spots | Notes |
|---|---|---|---|
| Spotiflow | Segmentation and Spot Detection Dataset | Segmentation and Spot Detection Results | Same dataset as `Classical Methods` and `Cellpose`, generated from CCDB_6843 |
| Spotiflow – Finetuning Dataset | Spotiflow Finetuning Dataset | – | From Spotiflow example notebook, MERFISH dataset from Zhang et al, 2021 |
06 - Measurement & Quantification
| Item | Dataset | Segmentation/Spots | Notes |
|---|---|---|---|
| Measurement Pipeline | Segmentation and Spot Detection Dataset | Segmentation and Spot Detection Results | Same dataset as `Classical Methods` and `Cellpose`, generated from CCDB_6843 |
| Nested Measurements | Group Work Dataset | (included in dataset) | – |
| Background Correction | Background Correction Dataset | – | – |
07 - Colocalization
| Item | Dataset | Segmentation/Spots | Notes |
|---|---|---|---|
| Pixel Intensity Based | Manders & Pearson's Colocalization Dataset | – | – |
| Object Based | Object Based Colocalization Dataset | – | – |
| Spatial Statistics | Segmentation and Spot Detection Dataset | Segmentation and Spot Detection Results | Same dataset as `Classical Methods`, `Cellpose` and `Spotiflow`, generated from CCDB_6843 |
BoBiac Exercises#
| Item | Dataset | Segmentation/Spots | Notes |
|---|---|---|---|
| Group Work 1: Building your Own Segmentation and Spot Detection Pipeline | Group Work 1 Dataset | (included in dataset) | – |
| Group Work 2: Analysing Oscillations in Time-Series Images | Group Work 2 Dataset | (included in dataset) | – |
| Group Work 3: Colocalization Analysis | Segmentation and Spot Detection Dataset | Segmentation and Spot Detection Results | Use the results from `Classical Methods`, `Cellpose` and `Spotiflow` notebooks if you have them. Same dataset as `Classical Methods`, `Cellpose` and `Spotiflow`, generated from CCDB_6843 |