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slideLookup
slideLookup
is designed to perform a whole-slide image (WSI) sample lookup (--samples
) in a directory or a set of directories (--dir
) containing WSI for a given --study_type
(AE or AAA). By default, the script will look for the following directories: CD3
, CD34
, CD66b
, CD68
, EVG
, FIBRIN
, GLYCC
, HE
, SMA
, SR
, SR_POLARIZED
. These can be changed with the --dir
flag. By default a log file is written to the current working directory
and is of the form [todays_date
.study_type
.slideLookup.log
.log].
Optionally, the found files can be copied (--copy
) to another directory (--copy-dir
). By default, the
files will be copied to the following directory: ../VirtualSlides/Projects/histo_lookups
. The --log
flag will change the
default output name of the log file, and --copy-dir
will change the log-output directory too. It provides
extra information (--verbose
) if requested.
Example usage:
python slideLookup.py --study_type AE --samples AE4211 AE3422 --dir CD14 CD3 --verbose
Argument(s):
-
--samples
,-s
- List of whole-slide image (WSI) samples, e.g.
AE4211
AE3422
. Required.
- List of whole-slide image (WSI) samples, e.g.
-
--dir
,-d
- List of directories, e.g.
CD14
CD3
. Required. Default:CD3
,CD34
,CD66b
,CD68
,EVG
,FIBRIN
,GLYCC
,HE
,SMA
,SR
,SR_POLARIZED
.
- List of directories, e.g.
-
--study_type
,-t
- Specify the study type prefix, e.g.,
AE
orAAA
(no other option is possible). Required.
- Specify the study type prefix, e.g.,
Optional argument(s):
-
--log
,-l
- Specify the log-filename which will be of the form [
todays_date
.study_type
.slideLookup.log
.log]. Optional. By default the log file will be written to the current working directory.
- Specify the log-filename which will be of the form [
-
--copy
,-c
- Copy files to copy-dir. Optional.
-
--copy_dir
,-cd
- Specify the directory to copy files to. Optional. By default the files will be copied to the following directory:
../VirtualSlides/Projects/histo_lookups
.
- Specify the directory to copy files to. Optional. By default the files will be copied to the following directory:
-
--verbose
,-v
- Print extra information. Optional.
-
--version
,-V
- Print version. Optional.
-
--help
,-h
- Print help message. Optional.
Licence. The MIT License (MIT): http://opensource.org/licenses/MIT.
Copyright (c) 2014-2023, Bas G.L. Nelissen & Sander W. van der Laan, UMC Utrecht, Utrecht, the Netherlands.
Introduction
General instructions
slide2Tiles
slideAppend.sh
slideAppendGCT.sh
slideConvert
slideDirectory
slideDupIdentify.py
slideEMask
slideEntropySegmentation.py
slideExtract.py
slideExtractTiles.py
slideInfo
slideInfo.py
slideJobChecker
slideLookup
slideMacro
slideMacro.py
slideMask
slideNormalize
slideRename
slideRename.py
slideThumb
slideThumb.py
slideQuantify_v1
slideQuantify_v1_1_expresshist_mask.sh
slideQuantify_v1_2_expresshist_tile.sh
slideQuantify_v1_3_tile_normalizing.sh
slideQuantify_v1_4_cellprofiler.sh
slideQuantify_v1_5_wrapup.sh
slideQuantify_v2
slideQuantify_v2_1_entropy_segmentation.sh
slideQuantify_v2_2_extract_tiles.sh
slideQuantify_v2_3_tile_normalizing.sh
slideQuantify_v2_4_cellprofiler.sh
slideQuantify_v2_5_wrapup.sh
slideQuantifyOSX
slideQuantify_cellprofiler.sh
slideQuantify_mask.sh
slideQuantify_normalizing.sh
slideQuantify_tiling.sh
slideQuantify_wrapup.sh
Conda version (default/preferred)
Homebrew version
Rocky 8 Conda version (default/preferred)
Ubuntu 16.04 LTS
Ubuntu 12.04
CentOS7 Conda version with modules
Administrator version