diff --git a/BeginnerSegmentation/bonus_materials.zip b/BeginnerSegmentation/bonus_materials.zip index 46a461a9..f0451ee4 100644 Binary files a/BeginnerSegmentation/bonus_materials.zip and b/BeginnerSegmentation/bonus_materials.zip differ diff --git a/BeginnerSegmentation/bonus_materials/beginner_segmentation_bonus_exercises.pdf b/BeginnerSegmentation/bonus_materials/beginner_segmentation_bonus_exercises.pdf index 43d7a803..e258d711 100644 Binary files a/BeginnerSegmentation/bonus_materials/beginner_segmentation_bonus_exercises.pdf and b/BeginnerSegmentation/bonus_materials/beginner_segmentation_bonus_exercises.pdf differ diff --git a/README.md b/README.md index 00167d82..f5754a9a 100644 --- a/README.md +++ b/README.md @@ -16,6 +16,12 @@ A tutorial that uses a CellPainting assay to find segmentation parameters for l Download button +### Bonus materials + +We have also created bonus materials designed to go with this tutorial - in these exercises, you will practice using CellProfiler to interface with other software tools like ilastik and Cellpose. + +Download button + En español: diff --git a/internal_use/docs/source/BeginnerSegmentation/BeginnerSegmentationPlugins.md b/internal_use/docs/source/BeginnerSegmentation/BeginnerSegmentationPlugins.md index 61af5fbe..dd9e015e 100644 --- a/internal_use/docs/source/BeginnerSegmentation/BeginnerSegmentationPlugins.md +++ b/internal_use/docs/source/BeginnerSegmentation/BeginnerSegmentationPlugins.md @@ -31,13 +31,8 @@ You can visit plugins.cellprofiler.org to learn more. To quote from that site: >- it requires extra libraries or other dependencies we are unable or unwilling to require for CellProfiler >- it has been contributed by a community member -```{tip} -- While that documentation has instructions for [installing plugins](https://plugins.cellprofiler.org/using_plugins.html#installing-plugins-without-dependencies), in step 2 it suggests downloading all of the CellProfiler plugins; this isn't a bad thing to do, but you can download individual plugins from GitHub with the website button below as well or instead. -``` - ````{tip} -- We strongly recommend making a dedicated folder to store your CellProfiler plugins, as loading can be slow if there are a lot of other miscellaneous files around (such if they sit in the Downloads folder, for example). - +While that documentation has instructions for [installing plugins](https://plugins.cellprofiler.org/using_plugins.html#installing-plugins-without-dependencies), in step 2 it suggests downloading all of the CellProfiler plugins; this isn't a bad thing to do, but you can download individual plugins from GitHub with the website button below as well or instead. ```{figure} ./TutorialImages/GitHubDownloadButton.png :width: 400 :align: center @@ -46,6 +41,10 @@ GitHub's "Download Raw Files" button ``` ```` +```{tip} +We strongly recommend making a dedicated folder to store your CellProfiler plugins, as loading can be slow if there are a lot of other miscellaneous files around (such if they sit in the Downloads folder, for example). +``` + ### Docker Desktop In Exercise 3 (and for Windows users, optionally Excercise 2 as well), we want to access software that we either don't want to install locally because it's painful if you're not pretty comfortable in Python (Cellpose) or that we CAN install locally but may not play nicely with other tools' multiprocessing setup (ilastik).