peng-lab · jenna-tomkinson · Aug 2, 2023 · Aug 2, 2023
diff --git a/README.md b/README.md
@@ -26,11 +26,11 @@ Reference:
 
 |Notebook|Description|Colab Link|
 | :------------------------: |:---------------:| :---------------------------------------------------: |
-| [timelapse_brightfield](https://github.com/peng-lab/BaSiCPy/tree/dev/docs/notebooks/timelapse_brightfield.ipynb)| 100 continuous brightfield frames of a time-lapse movie of differentiating mouse hematopoietic stem cells. | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/peng-lab/BaSiCPy/blob/dev/docs/notebooks/timelapse_brightfield.ipynb) |
-| [timelapse_nanog](https://github.com/peng-lab/BaSiCPy/tree/dev/docs/notebooks/timelapse_nanog.ipynb)| 189 continuous fluorescence frames of a time-lapse movie of differentiating mouse embryonic stem cells, which move much more slower compared to the fast moving hematopoietic stem cells, resulting in a much larger correlation between frames. Note that in this challenging case, the automatic parameters are no longer optimal, so we use the manual parameter setting (larger smooth regularization on both flat-field and dark-field) to improve BaSiC’s performance. | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/peng-lab/BaSiCPy/blob/dev/docs/notebooks/timelapse_nanog.ipynb) |
-| [WSI_brain](https://github.com/peng-lab/BaSiCPy/tree/dev/docs/notebooks/WSI_brain.ipynb)| you can stitch image tiles together to view the effect of shading correction | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/peng-lab/BaSiCPy/blob/dev/docs/notebooks/WSI_brain.ipynb) |
+| [timelapse_brightfield](./docs/notebooks/timelapse_brightfield.ipynb)| 100 continuous brightfield frames of a time-lapse movie of differentiating mouse hematopoietic stem cells. | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/peng-lab/BaSiCPy/blob/dev/docs/notebooks/timelapse_brightfield.ipynb) |
+| [timelapse_nanog](./docs/notebooks/timelapse_nanog.ipynb)| 189 continuous fluorescence frames of a time-lapse movie of differentiating mouse embryonic stem cells, which move much more slower compared to the fast moving hematopoietic stem cells, resulting in a much larger correlation between frames. Note that in this challenging case, the automatic parameters are no longer optimal, so we use the manual parameter setting (larger smooth regularization on both flat-field and dark-field) to improve BaSiC’s performance. | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/peng-lab/BaSiCPy/blob/dev/docs/notebooks/timelapse_nanog.ipynb) |
+| [WSI_brain](./docs/notebooks/WSI_brain.ipynb)| you can stitch image tiles together to view the effect of shading correction | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/peng-lab/BaSiCPy/blob/dev/docs/notebooks/WSI_brain.ipynb) |
 
-You can also find examples of running the package at [notebooks folder](https://github.com/peng-lab/BaSiCPy/tree/dev/docs/notebooks). Data used in the examples and a description can be downloaded from [Zenodo](https://doi.org/10.5281/zenodo.6334809).
+You can also find examples of running the package at [notebooks folder](./docs/notebooks/). Data used in the examples and a description can be downloaded from [Zenodo](https://doi.org/10.5281/zenodo.6334809).
 
 ---
 ## Usage

diff --git a/docs/notebooks/WSI_brain.ipynb b/docs/notebooks/WSI_brain.ipynb
diff --git a/docs/notebooks/timelapse_brightfield.ipynb b/docs/notebooks/timelapse_brightfield.ipynb
diff --git a/docs/notebooks/timelapse_nanog.ipynb b/docs/notebooks/timelapse_nanog.ipynb