Run image analysis and IBP on new data#9
Open
jenna-tomkinson wants to merge 1 commit intoWayScience:mainfrom
Open
Run image analysis and IBP on new data#9jenna-tomkinson wants to merge 1 commit intoWayScience:mainfrom
jenna-tomkinson wants to merge 1 commit intoWayScience:mainfrom
Conversation
|
Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
MattsonCam
approved these changes
Mar 19, 2026
Member
MattsonCam
left a comment
MattsonCam
left a comment
There was a problem hiding this comment.
LGTM @jenna-tomkinson, good job!
| channels: | ||
| - conda-forge | ||
| dependencies: | ||
| - conda-forge::python=3.9.12 |
Member
There was a problem hiding this comment.
This could cause environment drift, consider keeping a pin if possible
Comment on lines
+177
to
+197
| Output file location:Default Output Folder|/media/18tbdrive/1.Github_Repositories/nuclear_speckle_image_profiling/1.wave2_data/1.illumination_correction/test_ic | ||
| Image bit depth:16-bit integer | ||
| Overwrite existing files without warning?:No | ||
| When to save:Every cycle | ||
| Record the file and path information to the saved image?:No | ||
| Create subfolders in the output folder?:No | ||
| Base image folder:Elsewhere...| | ||
| How to save the series:T (Time) | ||
| Save with lossless compression?:Yes | ||
|
|
||
| SaveImages:[module_num:12|svn_version:'Unknown'|variable_revision_number:16|show_window:False|notes:['Save the corrected images with a suffix.']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False] | ||
| Select the type of image to save:Image | ||
| Select the image to save:CorrSON | ||
| Select method for constructing file names:From image filename | ||
| Select image name for file prefix:SON | ||
| Enter single file name:OrigBlue | ||
| Number of digits:4 | ||
| Append a suffix to the image file name?:Yes | ||
| Text to append to the image name:_illumcorrect | ||
| Saved file format:tiff | ||
| Output file location:Default Output Folder| |
Member
There was a problem hiding this comment.
Consider making these Output file locations the same if it makes sense, and if possible, making the path non-machine-specific
| To run the CellProfiler analysis pipeline, run the command below: | ||
|
|
||
| ```bash | ||
| # Make sure that you are in the 3.cp_analysis folder in terminal |
Member
There was a problem hiding this comment.
Suggested change
| # Make sure that you are in the 3.cp_analysis folder in terminal | |
| # Make sure that you are in the 2.cp_analysis folder in terminal |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
In this PR, image analysis and IBP pipelines are applied to the new U2OS data. Profiles are added to
bandicoot.