Updated requirements

Author: fercer

README.md

@@ -24,20 +24,22 @@ Install the following packages in the newly created environment.
 ```
 conda activate scale-up
 
-conda install -c conda-forge "cellpose>=3.0,<4.0" tifffile=2025.6.11 "zarr>=2.0,<3.0" dask=2025.5.1 imagecodecs=2025.3.30
+conda install -c conda-forge "cellpose>=3.0,<4.0" tifffile=2025.6.11 "zarr>=2.0,<3.0" dask=2025.5.1 distributed=2025.5.1 dask-image=2024.5.3 imagecodecs=2025.3.30
 ```
 
-We might need to open some image files that are compressed using `JPEG2000`, to do that we'll use `imagecodecs` to have access to this compression algorithm.
+We'll open some image files that are compressed using `JPEG2000`, so we need `imagecodecs` to have access to this compression algorithm.
 
-Additionally, install Jupyterlab to follow the notebooks.
+Additionally, install Jupyterlab to follow the notebooks, and its Dask extension.
 
 ```
-conda activate scale-up
-
-conda install -c conda-forge jupyterlab=4.4.3
+conda install -c conda-forge jupyterlab=4.4.3 dask-labextension=7.0.0
 ```
 
 ## A test image
 
 We'll work with big microscopy images. An example of that kind of image can be found [here](https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1.svs).
 So it is a good idea to have it downloaded as well.
+
+A crop of that image can be found [here](https://drive.google.com/file/d/17owNcq_Or6aBAyUVE33fyHSS0VvKuHSw/view?usp=sharing), along with its `Zarr` version [here](https://drive.google.com/file/d/1BmNxOrO3vOFPR-PCnV00DYgFsD1sDu47/view?usp=sharing).
+
+A smaller example image can be found [here](https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1-Small-Region.svs), and its corresponding `Zarr` version is [here](https://drive.google.com/file/d/1MifgafB5mhVAvqjzEAAR_zQajAU5Dcya/view?usp=drive_link).

requirements.md

@@ -1,3 +1,6 @@
+# SciPy 2025 - Tutorial: Scaling-up deep learning inference to large-scale bioimage data
+Tutorial about scaling-up image analysis with Dask presented during SciPy 2025 Conference (July 7-13, 2025)
+
 # Installation instructions
 
 This workshop uses Dask, Zarr, TiffFile, and Cellpose libraries.
@@ -21,16 +24,22 @@ Install the following packages in the newly created environment.
 ```
 conda activate scale-up
 
-conda install -c conda-forge "cellpose>=3.0,<4.0" "tifffile[all]<=2025.5.21" "zarr>=2.0,<3.0" dask=2025.5.1 distributed=2025.5.1  jupyterlab=4.4.3 bioformats2raw=0.9.4
+conda install -c conda-forge "cellpose>=3.0,<4.0" tifffile=2025.6.11 "zarr>=2.0,<3.0" dask=2025.5.1 distributed=2025.5.1 dask-image=2024.5.3 imagecodecs=2025.3.30
 ```
 
-We'll convert an image from Tiff format to the Zarr format, so make sure to install `bioformats2raw` as follows inside the same `scale-up` environment:
+We'll open some image files that are compressed using `JPEG2000`, so we need `imagecodecs` to have access to this compression algorithm.
+
+Additionally, install Jupyterlab to follow the notebooks, and its Dask extension.
 
 ```
-conda install -c ome bioformats2raw=0.9.4
+conda install -c conda-forge jupyterlab=4.4.3 dask-labextension=7.0.0
 ```
 
 ## A test image
 
 We'll work with big microscopy images. An example of that kind of image can be found [here](https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1.svs).
 So it is a good idea to have it downloaded as well.
+
+A crop of that image can be found [here](https://drive.google.com/file/d/17owNcq_Or6aBAyUVE33fyHSS0VvKuHSw/view?usp=sharing), along with its `Zarr` version [here](https://drive.google.com/file/d/1BmNxOrO3vOFPR-PCnV00DYgFsD1sDu47/view?usp=sharing).
+
+A smaller example image can be found [here](https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1-Small-Region.svs), and its corresponding `Zarr` version is [here](https://drive.google.com/file/d/1MifgafB5mhVAvqjzEAAR_zQajAU5Dcya/view?usp=drive_link).