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Fix Plate_3_prime metadata plate column bug in CellProfiler #48

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merged 3 commits into from
Jun 14, 2024
Merged

Fix Plate_3_prime metadata plate column bug in CellProfiler #48

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7924f73
update plate3prime metadata plate column bug
jenna-tomkinson Jun 14, 2024
2766d07
update code to revert back from only processing plate3prime
jenna-tomkinson Jun 14, 2024
5fcebfa
add nbconvert
jenna-tomkinson Jun 14, 2024
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2 changes: 1 addition & 1 deletion 2.cellprofiler_analysis/NF1_analysis_4channel.cppipe
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ Metadata:[module_num:2|svn_version:'Unknown'|variable_revision_number:6|show_win
Metadata extraction method:Extract from file/folder names
Metadata source:Folder name
Regular expression to extract from file name:^(?P<Plate>.*)_(?P<Well>[A-P][0-9]{2})_s(?P<Site>[0-9])_w(?P<ChannelNumber>[0-9])
Regular expression to extract from folder name:Corrected_(?P<Plate>Plate_[0-9]{1})
Regular expression to extract from folder name:Corrected_(?P<Plate>Plate_3_prime|Plate_3|Plate_4|Plate_5)
Extract metadata from:All images
Select the filtering criteria:and (file does contain "")
Metadata file location:Elsewhere...|
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2 changes: 1 addition & 1 deletion 2.cellprofiler_analysis/analysis_output/Plate_3_prime/Plate_3_prime_nf1_analysis.sqlite
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12 changes: 3 additions & 9 deletions 2.cellprofiler_analysis/nf1_analysis.ipynb
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Expand Up @@ -89,15 +89,9 @@
"name": "stdout",
"output_type": "stream",
"text": [
"{ 'Plate_3': { 'path_to_images': PosixPath('/home/jenna/nf1_cellpainting_data/1.cellprofiler_ic/Corrected_Images/Corrected_Plate_3'),\n",
" 'path_to_output': PosixPath('analysis_output/Plate_3'),\n",
" 'path_to_pipeline': PosixPath('/home/jenna/nf1_cellpainting_data/2.cellprofiler_analysis/NF1_analysis_4channel.cppipe')},\n",
" 'Plate_3_prime': { 'path_to_images': PosixPath('/home/jenna/nf1_cellpainting_data/1.cellprofiler_ic/Corrected_Images/Corrected_Plate_3_prime'),\n",
"{ 'Plate_3_prime': { 'path_to_images': PosixPath('/home/jenna/nf1_cellpainting_data/1.cellprofiler_ic/Corrected_Images/Corrected_Plate_3_prime'),\n",
" 'path_to_output': PosixPath('analysis_output/Plate_3_prime'),\n",
" 'path_to_pipeline': PosixPath('/home/jenna/nf1_cellpainting_data/2.cellprofiler_analysis/NF1_analysis_4channel.cppipe')},\n",
" 'Plate_4': { 'path_to_images': PosixPath('/home/jenna/nf1_cellpainting_data/1.cellprofiler_ic/Corrected_Images/Corrected_Plate_4'),\n",
" 'path_to_output': PosixPath('analysis_output/Plate_4'),\n",
" 'path_to_pipeline': PosixPath('/home/jenna/nf1_cellpainting_data/2.cellprofiler_analysis/NF1_analysis_4channel.cppipe')}}\n"
" 'path_to_pipeline': PosixPath('/home/jenna/nf1_cellpainting_data/2.cellprofiler_analysis/NF1_analysis_4channel.cppipe')}}\n"
]
}
],
Expand All @@ -110,7 +104,7 @@
" ).resolve(strict=True),\n",
" \"path_to_output\": pathlib.Path(f\"{output_dir}/{name}\"),\n",
" }\n",
" for name in plate_names if name in [\"Plate_3\", \"Plate_3_prime\", \"Plate_4\"] # focus on Plate_3, Plate_3_prime, and Plate_4\n",
" for name in plate_names if name in [\"Plate_3_prime\"] # focus on Plate_3_prime\n",
"}\n",
"\n",
"# iterate over the dictionary and add the path_to_pipeline specific for each plate\n",
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2 changes: 1 addition & 1 deletion 2.cellprofiler_analysis/scripts/nf1_analysis.py
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Expand Up @@ -55,7 +55,7 @@
).resolve(strict=True),
"path_to_output": pathlib.Path(f"{output_dir}/{name}"),
}
for name in plate_names if name in ["Plate_3", "Plate_3_prime", "Plate_4"] # focus on Plate_3, Plate_3_prime, and Plate_4
for name in plate_names if name in ["Plate_3_prime"] # focus on Plate_3_prime
}

# iterate over the dictionary and add the path_to_pipeline specific for each plate
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