CellProfiler · bethac07 · Oct 27, 2025 · Oct 27, 2025
diff --git a/internal_use/docs/_build/gettext/BeginnerSegmentation.pot b/internal_use/docs/_build/gettext/BeginnerSegmentation.pot
@@ -8,7 +8,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: cellprofiler-tutorials \n"
 "Report-Msgid-Bugs-To: \n"
-"POT-Creation-Date: 2025-10-21 11:14+0000\n"
+"POT-Creation-Date: 2025-10-27 00:08+0000\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <LL@li.org>\n"
@@ -37,7 +37,7 @@ msgid "Download and install [Docker Desktop](https://www.docker.com/products/doc
 msgstr ""
 
 #: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:10
-msgid "Download at least one RunCellpose Docker and one ilastik Docker from Dockerhub. This will happen automatically the first time you call a given Docker from CellProfiler (i.e. run a CellProfiler pipeline that uses the Docker) but if you are running this tutorial in a workshop setting we strongly recommend download in advance of the workshop as these are large files (5-10 GB) and bandwidth is often limited in a workshop setting. In Docker Desktop or Podman Desktop you can search for containers in the top search bar (see below). Make sure you select a tag (version) that is supported by the plugin you are using and then select \"Pull\". We reccomend `biocontainers/ilastik:1.4.0_cv2` for ilastik and `cellprofiler/runcellpose_with_pretrained:3.1.2.2` or `cellprofiler/runcellpose_with_pretrained:4.0.6` for Cellpose."
+msgid "Download at least one RunCellpose Docker and one ilastik Docker from Dockerhub. This will happen automatically the first time you call a given Docker from CellProfiler (i.e. run a CellProfiler pipeline that uses the Docker) but if you are running this tutorial in a workshop setting we strongly recommend download in advance of the workshop as these are large files (5-10 GB) and bandwidth is often limited in a workshop setting. In Docker Desktop or Podman Desktop you can search for containers in the top search bar (see below). Make sure you select a tag (version) that is supported by the plugin you are using and then select \"Pull\". We recommend `biocontainers/ilastik:1.4.0_cv2` for ilastik and `cellprofiler/runcellpose_with_pretrained:3.1.2.2` for Cellpose."
 msgstr ""
 
 #: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:15
@@ -381,17 +381,17 @@ msgid "If you have ilastik installed on your machine you can set the path to you
 msgstr ""
 
 #: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:252
-#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:321
+#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:323
 msgid "You may wish to put a pause <img src=\"./TutorialImages/Pause.png\" width=\"20\" alt=\"Pause\"/> next to SaveImages, or uncheck it <img src=\"./TutorialImages/InactivatedModule.png\" width=\"20\" alt=\"Unchecked\"/>, to keep it from saving images while you are exploring this pipeline."
 msgstr ""
 
 #: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:252
-#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:321
+#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:323
 msgid "Pause"
 msgstr ""
 
 #: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:252
-#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:321
+#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:323
 msgid "Unchecked"
 msgstr ""
 
@@ -408,7 +408,7 @@ msgid "Eye Open icon"
 msgstr ""
 
 #: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:253
-#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:320
+#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:322
 msgid "Run"
 msgstr ""
 
@@ -521,7 +521,7 @@ msgid "Load the pipeline and evaluate segmentation"
 msgstr ""
 
 #: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:314
-msgid "If using Docker, the very first time you execute the RunCellpose module, it will need to download a ~5GB-10GB file (depending on the verison of Cellpose), which may be slow depending on your internet connection (unless you downloaded it in preparation as we suggest above). You only need to do this step once, however!"
+msgid "If using Docker/Podman, the very first time you execute the RunCellpose module, it will need to download a ~5GB-10GB file (depending on the verison of Cellpose), which may be slow depending on your internet connection (unless you downloaded it in preparation as we suggest above). You only need to do this step once, however!"
 msgstr ""
 
 #: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:318
@@ -533,82 +533,90 @@ msgid "Drag the `images_Illum-corrected` subfolder from the main exercise into t
 msgstr ""
 
 #: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:320
-msgid "Put CellProfiler into TestMode <img src=\"./TutorialImages/startTestMode.png\" width=\"120\" alt=\"Start Test Mode button\"/>, open the eye icons <img src=\"./TutorialImages/EyeOpen.png\" width=\"20\" alt=\"Open Eye icon\"/> next to RunCellpose and OverlayOutlines, and then hit Run <img src=\"./TutorialImages/Run.png\" width=\"120\" alt=\"Run\"/>"
+msgid "Put CellProfiler into TestMode <img src=\"./TutorialImages/startTestMode.png\" width=\"120\" alt=\"Start Test Mode button\"/>"
 msgstr ""
 
 #: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:320
 msgid "Start Test Mode button"
 msgstr ""
 
-#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:320
-msgid "Open Eye icon"
+#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:321
+msgid "If using Docker/Podman, and if you've already pre-downloaded a container, ensure that the `Select Cellpose Docker image` setting in the `RunCellpose` module matches the container you already downloaded."
+msgstr ""
+
+#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:322
+msgid "Open the eye icons <img src=\"./TutorialImages/EyeOpen.png\" width=\"20\" alt=\"Open Eye icon\"/> next to RunCellpose and OverlayOutlines, and then hit Run <img src=\"./TutorialImages/Run.png\" width=\"120\" alt=\"Run\"/>"
 msgstr ""
 
 #: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:322
+msgid "Open Eye icon"
+msgstr ""
+
+#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:324
 msgid "As before, using OverlayOutlines and/or the WorkspaceViewer, evaluate segmentation on a few images. Where is CellProfiler doing better, and where is Cellpose doing better?"
 msgstr ""
 
-#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:323
+#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:325
 msgid "Use the Info <img src=\"./TutorialImages/Info.png\" width=\"35\" alt=\"Info\"/> button to learn more about the different parameters you can pass to Cellpose (we don't offer all of them, but many!) - how does tweaking these affect your output? How about changing the model you're using, and/or the image you're segmenting?"
 msgstr ""
 
-#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:323
+#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:325
 msgid "Info"
 msgstr ""
 
-#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:329
+#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:331
 msgid "The output of the RunCellpose module"
 msgstr ""
 
-#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:332
+#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:334
 msgid "Bonus-to-the-Bonus 1 - test on a more varied data set"
 msgstr ""
 
-#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:334
+#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:336
 msgid "The data we gave you in this exercise was all very clean, and all from the negative control wells of this experiment. The [folder linked here](https://drive.google.com/file/d/10kZMhr2bVR14vMP7kG5iZGujjUI3Nn3Y/view?usp=sharing) contains images with a broader variety of phenotypes - try replacing the images in the `Images` module with this folder instead and see how well the two kinds of segmentation work in different conditions!"
 msgstr ""
 
-#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:340
+#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:342
 msgid "A broader range of phenotypes can be harder to consistently account for in conducting segmentation."
 msgstr ""
 
-#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:344
+#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:346
 msgid "You’re encouraged to explore the performance in some random images on your own (you can do this from the `Test` menu with the `Random Image Set` option), but if you find yourself consistently ending up with images that look similar you can try examining images from the following list of wells- A08, A12, B12, B18, C7, D6, D19, D22, E3. You can pick these with `Test` -> `Choose Image Set`"
 msgstr ""
 
-#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:348
+#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:350
 msgid "Bonus-to-the-Bonus 2 - improve Cellpose segmentation"
 msgstr ""
 
-#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:350
+#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:352
 msgid "Based on your evaluations above, can you identify some places where additional training might help fix some issues in the Cellpose model? If you happen to have Cellpose on your computer (or want to try installing it - see Exercise 1 for a link to the official install instructions), open Cellpose with some of the `Ch1` images and see if you can train a model that will perform better."
 msgstr ""
 
-#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:353
+#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:355
 msgid "Bonus-to-the-Bonus 3 - test your classical segmentation skills"
 msgstr ""
 
-#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:355
+#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:357
 msgid "The classical segmentation parameters provided here are based on expert tuning from a very experienced CellProfiler user - how close can you get? Add another IdentifyPrimaryObjects module to the pipeline, tune it yourself, and then look in the workspace viewer to see how it performs, especially in the more diverse image set from Bonus-to-the-Bonus 1. Compare your parameters to the expert ones - how do they differ? Do you understand why some of these settings may have been chosen?"
 msgstr ""
 
-#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:360
+#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:362
 msgid "What next? Want to know more about CellProfiler plugins and modules?"
 msgstr ""
 
-#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:362
+#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:364
 msgid "Read the [CellProfiler-plugins paper](https://pubmed.ncbi.nlm.nih.gov/37690102/)."
 msgstr ""
 
-#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:363
+#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:365
 msgid "Read the [CellProfiler-plugins documentation](https://plugins.cellprofiler.org/)."
 msgstr ""
 
-#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:364
+#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:366
 msgid "Watch this [video](https://www.youtube.com/watch?v=fgF_YueM1b8) to learn how to write a module."
 msgstr ""
 
-#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:365
+#: ../../source/BeginnerSegmentation/BeginnerSegmentationPlugins.md:367
 msgid "Watch this [Ask Erin Dear Beth video podcast](https://youtu.be/31iK-ETKtFM) to learn more about plugins."
 msgstr ""