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Pull request from dev into master #51

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Merged
ayakimovich merged 3 commits into from
Aug 6, 2025
Merged

Pull request from dev into master #51

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dd65fdf
Merge pull request #50 from plaque2/master
ayakimovich Aug 1, 2025
e309cfa
updation of data link for fluorescence microscopy images
trinade Aug 4, 2025
09f8b8c
updation of version in setup.py
trinade Aug 6, 2025
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30 changes: 28 additions & 2 deletions notebooks/load_data.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@
}
],
"source": [
"!curl https://rodare.hzdr.de/record/3003/files/VACVPlaque_test.zip -o ../../../../data_backup/VACVPlaque_test.zip \n"
"!curl https://rodare.hzdr.de/record/3003/files/VACVPlaque_test.zip -o ../../../data_backup/VACVPlaque_test.zip \n"
]
},
{
Expand Down Expand Up @@ -132,13 +132,39 @@
"###### We again use the RODARE link to download the high-content 384-well plate fluorescence microscopy data that is used in the `Fluorescence Microscopy Analysis` detailed in the fp_detailed.ipynb, fp_starter.ipynb and example_analysis.ipynb notebooks. Here we have used `curl` which comes preinstalled in MacOS but `wget` for MacOS, Linux and Windows can be equivalently used as well."
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
" % Total % Received % Xferd Average Speed Time Time Time Current\n",
" Dload Upload Total Spent Left Speed\n",
" 3 9306M 3 340M 0 0 5410k 0 0:29:21 0:01:04 0:28:17 7064k048k 0 0:19:44 0:00:11 0:19:33 7195k 0:27:17 0:00:33 0:26:44 6526k 0 5156k 0 0:30:47 0:00:56 0:29:51 5931k^C\n"
]
}
],
"source": [
"!curl https://rodare.hzdr.de/record/3900/files/cov_raw.zip -o ../../../data_backup/cov_raw.zip"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"!curl https://rodare.hzdr.de/record/3742/ -o ../../../../data_backup/fluorescence.zip"
"!unzip ../../../data_backup/cov_raw.zip -d ../../../data_backup/cov_raw/"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"###### These now correspond to 384-well fluorescence microscopy images as used in the `fp_detailed`, `fp_starter` and `example_anaalysis` notebooks as mentioned in the the paper. ```cov_raw``` would be the ```base_dir``` used in these notebooks."
]
}
],
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2 changes: 1 addition & 1 deletion setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
# Get the long description from the README file
long_description = (cwd / 'README.md').read_text(encoding='utf-8')

version = 'v0.2.2'
version = 'v0.2.3'

setup(
name = 'PyPlaque',
Expand Down