diff --git a/docs/source/_static/comparison_tensorflow.png b/docs/source/_static/comparison_tensorflow.png new file mode 100644 index 00000000..bd5006ca Binary files /dev/null and b/docs/source/_static/comparison_tensorflow.png differ diff --git a/docs/source/_static/comparison_torch.png b/docs/source/_static/comparison_torch.png new file mode 100644 index 00000000..17912763 Binary files /dev/null and b/docs/source/_static/comparison_torch.png differ diff --git a/docs/source/blog/cellfinder-v1_3.md b/docs/source/blog/cellfinder-v1_3.md new file mode 100644 index 00000000..01139bc5 --- /dev/null +++ b/docs/source/blog/cellfinder-v1_3.md @@ -0,0 +1,51 @@ +--- +blogpost: true +date: June 3, 2024 +author: Igor Tatarnikov +location: London, England +category: brainglobe +language: English +--- + +# Cellfinder version 1.3.0 is released! + +We are excited to announce that a new version of `cellfinder` has been released. + +## Main updates + * This update brings a significant change to the backend of `cellfinder`, as we have switched from TensorFlow to PyTorch. This change allows `cellfinder` to support python versions 3.11+, and simplifies the installation process. The new `cellfinder` version maintains the same classification accuracy. Models trained using previous versions of `cellfinder` will continue to work with the new version. + + + * The default batch size used for detection has been increased to 64, which improves classification speed by approximately 40% on most systems. The batch size used for detection can now also be adjusted in the `napari` plugin. + +## What do I need to do? + +We recommend using a fresh conda environment to simplify the update. +For GPU support, please follow the installation instructions in the [documentation](../documentation/setting-up/gpu.md). + +```bash +conda create -n cellfinder -c conda-forge python=3.11 +conda activate cellfinder +pip install cellfinder +``` + +You can also update an existing installation of `cellfinder` using pip: + +```bash +pip install --upgrade cellfinder +``` + + +## Classification performance +The classification performance between the two versions is comparable. Below is a comparison of the performance between the two versions using data from the [`cellfinder` paper](https://doi.org/10.1371/journal.pcbi.1009074). Running `cellfinder` with a PyTorch backend results in a comparable Pearson correlation and slightly improved linear best-fit slope (labelled as "coeff" in the plot) when comparing to manual cell counts. For more details on how the plots were generated, see the [`cellfinder` paper](https://doi.org/10.1371/journal.pcbi.1009074). + +### TensorFlow backend + +
+ +
+ +### PyTorch backend + ++ +