Test Page

2021-03-08, SFN:
Test-page for internal development. Used for trying out different layouts and learning to use liquid

Filtering over array

Because keys may hold multiple values, e.g. tools: [fiji, matlab, ilastik] and we just want to find if a member has e.g. “fiji” listed

Filtering on association (“ETH Zurich”)

andrzej

sstoma

tarun

Filtering on tools (“fiji”)

simon [“fiji” “matlab” “ilastik”]

sstoma [“fiji” “python”]

Filtering on tools, algorithmically

Now combine this with algorithmic loop over individual tool values!!

Extract, into a variable/list/array/string, names of all individual tools given by all members
use concat (arrays) or append (strings) or prepend to build the variable
Loop over that variable
For each value of tool, print member name who contains it
utilize the uniq filter in liquid

Learn to filter out users with no tools listed:

andrzej has value of dummy-tool variable: [“python”]

simon has value of dummy-tool variable: [“fiji”“matlab”“ilastik”]

sstoma has value of dummy-tool variable: [“fiji”“python”]

Build array of all tools:

% comment %}

Value of alltools initialy: ["fiji", "fiji"]

Value of alltools in loop: ["fiji", "fiji", "[\"python\"]"]

Value of alltools in loop: ["fiji", "fiji", "[\"python\"]", "[\"fiji\"", " \"matlab\"", " \"ilastik\"]"]

Value of alltools in loop: ["fiji", "fiji", "[\"python\"]", "[\"fiji\"", " \"matlab\"", " \"ilastik\"]", "[\"fiji\"", " \"python\"]"]

remove “\”: [“fiji”, “fiji”, “[“python”]”, “[“fiji””, “ “matlab””, “ “ilastik”]”, “[“fiji””, “ “python”]”]
remove “\”, “[”: “fiji”, “fiji”, ““python”]”, ““fiji””, “ “matlab””, “ “ilastik”]”, ““fiji””, “ “python”]”]
remove “\”, “[”, “]”: “fiji”, “fiji”, ““python””, ““fiji””, “ “matlab””, “ “ilastik””, ““fiji””, “ “python””

Unique list: fiji[“python”][“fiji” “matlab” “ilastik”] “python”]
Unique list, inspected: ["fiji", "[\"python\"]", "[\"fiji\"", " \"matlab\"", " \"ilastik\"]", " \"python\"]"]

This doens’t really work: the combination of yaml and liquid is not a happy one.

% endcomment %}

`map` filter on `categories`

[“cat3” “cat4” “cat5”]
[“cat1” “cat2” “cat3”]
[“cat2” “cat3”]

Doesn’t work that well, since members is a collection and map seems built to work on a single page

`map` filter on “tools” keyword

	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	- python 
	
	- dummy: ["python"]
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	- fijimatlabilastik 
	
	- dummy: ["fiji""matlab""ilastik"]
	
	- fijipython 
	
	- dummy: ["fiji""python"]
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy: 
	
	-  
	
	- dummy:

inspect final item: nil
inspect final concat_tools: ["fiji", "fiji", "[\"python\"]", "[\"fiji\"", "\"matlab\"", "\"ilastik\"]", "[\"fiji\"", "\"python\"]"]

Doesn’t work well at all - again the issue of format of arrays - yaml and liquid not the same thing.

List of tools (new keyword)

["fiji", "matlab", "ilastik"]
["fiji", "python"]
["python"]

List of categories

[]
["cat1", "cat2", "cat3"]
["cat2", "cat3"]
["cat3", "cat4", "cat5"]

List of affiliations

BioVision Center
EPFL
ETH Zurich
ETHZ Basel
FMI Basel
Fenaco
Hôpitaux Universitaires Genève
IDIAP Martigny
Institute for Research in Biomedicine
Roche
University Hospital Zurich
University of Basel
University of Bern
University of Fribourg
University of Geneva
University of Lausanne
University of Zurich
X-members
unaffiliated

List of tags

[]
["CellProfiler", "QuPath", "Omero", "KNIME", "Imaris", "R"]
["DL", "Python", "Ubuntu", "Github", "TensorFlow", "PyTorch"]
["ImageJ / Fiji", "CellProfiler", "NAPARI", "Omero", "KNIME", "Imaris"]
["ImageJ / Fiji", "CellProfiler", "QuPath", "NAPARI", "Imaris", "Arivis"]
["ImageJ / Fiji", "CellProfiler", "QuPath", "ilastik", "ICY", "NAPARI", "Omero", "KNIME"]
["ImageJ / Fiji", "CellProfiler", "QuPath", "ilastik", "ICY", "NAPARI", "Omero", "KNIME", "Huygens", "Imaris", "Arivis", "R"]
["ImageJ / Fiji", "CellProfiler", "QuPath", "ilastik", "NAPARI", "Omero", "Imaris", "R"]
["ImageJ / Fiji", "CellProfiler", "ilastik", "NAPARI"]
["ImageJ / Fiji", "CellProfiler", "ilastik", "NAPARI", "R"]
["ImageJ / Fiji", "Imaris"]
["ImageJ / Fiji", "NAPARI", "Imaris"]
["ImageJ / Fiji", "QuPath", "NAPARI", "Omero", "Python"]
["ImageJ / Fiji", "QuPath", "ilastik", "NAPARI", "Omero"]
["Java", "Python", "Matlab", "C", "C++", "C#", "R"]
["Napari", "Fiji", "Julia", "R", "Python", "Scikit-image", "Linux"]
["Python", "Qt", "Matlab", "C++", "Qupath"]
["cat1", "cat2"]
["fiji"]
["fiji", "CellProfiler", "NAPARI", "KNIME"]
["fiji", "Python"]
["fiji", "cellprofiler", "ilastik", "napari", "KNIME", "python", "R", "Shiny"]
["fiji", "cellprofiler", "qupath", "ilastik", "napari", "KNIME", "imaris", "R", "python"]
["fiji", "imageJ", "omero"]
["fiji", "imagej"]
["fiji", "imagej", "hrm", "omero", "python", "qupath"]
["fiji", "imagej", "image.sc", "omero", "jupyter", "imaris", "arivis", "python", "git"]
["fiji", "imagej", "omero", "jupyter", "imaris", "arivis", "python"]
["fiji", "imagej", "qupath", "cellpose", "imagesc", "ilastik", "cellprofiler"]
["fiji", "imagej", "qupath", "image.sc", "ilastik", "cellprofiler", "cellprofiler analyst", "cellpose", "knime", "omero", "renku", "imaris", "icy"]
["fiji", "imaris"]
["fiji", "python", "jupyter", "ilastik", "pytorch", "scikit-image", "dask", "napari"]
["fiji", "qupath", "ilastik", "napari", "huygens", "imaris", "python", "groovy", "mathematica"]
["fiji", "qupath", "stardist", "cellpose", "imagesc", "ilastik"]
["ilastik", "NAPARI", "Python"]
["imagej", "fiji", "ilastik", "cellpose", "napari", "python", "matlab", "java"]
["matlab", "fiji"]
["python"]
["python", "C++", "CUDA", "TensorFlow", "Torch", "fiji", "ilastik", "napari", "imaris"]
["python", "fiji"]
["python", "matlab", "C#", "Java", "fiji", "napari", "cellprofiler", "ilastik", "huygens", "imaris"]
["python", "phaedra"]
["tensorflow/keras", "scikit-image", "OpenCV", "Ilastik", "ImageJ/Fiji", "NAPARI", "CellProfiler"]
["visiopharm", "definiens", "fiji", "qupath", "multiplex", "IHC"]

technotes 1
job-openings 1

technotes

Setting Up The Site

1 minute read

Notes from setting up the site on GitHub, with Jekyll on Ubuntu

job-openings

Job opening as Research associate in biomedical image analysis

2 minute read

We are looking for a highly motivated bioimage data analyst to join the lab of César Nombela-Arrieta, at the department of Medical Oncology and Hematology of...