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fix(pipeline): default file/folder naming to 'No' #155

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fda8f38
fix(pipeline): default file/folder naming to 'No'
NanoCelllab Feb 10, 2026
d7c548d
Update Nuclei3DTimeConsumingPipeline.md
labnanocell Feb 11, 2026
e646cd2
Update BBBC022_QualityControlExercise.md
labnanocell Feb 12, 2026
c84f531
Update BBBC022_QualityControlExercise.md
labnanocell Feb 12, 2026
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4 changes: 2 additions & 2 deletions 3DFISHinCelegans/NewFishPureCP.cppipe
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
CellProfiler Pipeline: http://www.cellprofiler.org
Version:5
DateRevision:421
DateRevision:428
GitHash:
ModuleCount:20
HasImagePlaneDetails:False
Expand Down Expand Up @@ -251,7 +251,7 @@ SaveImages:[module_num:19|svn_version:'Unknown'|variable_revision_number:16|show
ExportToSpreadsheet:[module_num:20|svn_version:'Unknown'|variable_revision_number:13|show_window:True|notes:[]|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
Select the column delimiter:Comma (",")
Add image metadata columns to your object data file?:No
Add image file and folder names to your object data file?:Yes
Add image file and folder names to your object data file?:No
Select the measurements to export:Yes
Calculate the per-image mean values for object measurements?:No
Calculate the per-image median values for object measurements?:No
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5 changes: 1 addition & 4 deletions internal_use/docs/source/3DNuclei/Nuclei3DTimeConsumingPipeline.md
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Expand Up @@ -19,8 +19,6 @@ and the clustering of their nuclei in 3D cell culture.

Voxel dimensions: 0.124x0.124x0.200 um

Calibration Image: Voxel dimensions: 1x1x1 um

## **Importing data in CellProfiler**

1. Highlight the **Images** module.
Expand Down Expand Up @@ -56,8 +54,7 @@ always a good practice to check if everything is fine.


>The relative pixel spacing was provided and is 0.124 um in x and y and
0.200 um in z. To run the calibration file please change the relative
pixel spacing to 1x1x1 um.
0.200 um in z.

6. Assign the images “variable names” that describe the contents in the image. For example, use the name "Nuclei", "DNA", “DAPI” or something else that will remind you what the image is.
7. Hit the "update" button to populate
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4 changes: 2 additions & 2 deletions internal_use/docs/source/QualityControl/BBBC022_QualityControlExercise.md
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Expand Up @@ -204,14 +204,14 @@ in later steps.
*Figure 1: Examining the objects inside a gate.*
```

- Look at some of the images inside the gate ( you may need to click
- Look at some of the images inside the gate (you may need to click
‘Show controls’ to adjust the zoom, contrast stretch, etc). Are they
in focus, and are they free of bright debris? If they seem all or
mostly like they’re high quality, adjust the gate to look at a
different/smaller subset or delete it altogether by using the Gate
Inspector (‘gate’-> ‘MANAGE GATES’).

## 4. **Optional- use the PlateViewer tool to check for other features to gate on (~10 minutes)**
## 4. **Optional — use the PlateViewer tool to check for other features to gate on (~10 minutes)**

If you want to see if you can find additional features that might distinguish good
images from bad images, feel free to explore the feature set more thoroughly.
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