DAPI/Oligo analysis for the Whistler lab.
Install of the code here is a little heavy as we are using rather cutting edge packages, including cellpose, aicsimageio, and napari.
- Create and activate a conda environment.
Assuming cellpose requires Python 3.8
conda create -y -n oligo-analysis python=3.8
Activate environment
conda activate oligo-analysis
Update pip
pip install --upgrade pip
- Install from requirements.txt
requirements.txt
- Some local installs are currently required. We will eventually remove this.
Make sure this is in my local dev branch
pip install ../napari-layer-table/.
We have created some pre-trained models, they are in the models/ folder.
To run the models on new image data and save a cellpose _seg.npy file, use batchRunFolder() in oligoAnalysis/oligoAnalysisFolder.py
This is required before you can fully use the main interface in oligoanalysis/interface/oligoInterface.py.
I have given up on this. When we switch to loading other files other than Zeiss czi, it won't work.
My original goal here was to load the date/time of image acquisition.
from aicsimageio import AICSImage
def readCzi():
# looking for
# Information|Document|CreationDate = 2022-09-22T15:03:58
from aicspylibczi import CziFile
cziPath = '/Users/cudmore/Dropbox/data/cudmore-fiji-plugins/test-data/shu-ling/pHA1_DsRed.czi'
with open(cziPath) as f:
czi = CziFile(f)
#print('czi:', [x for x in dir(czi)])
print(' czi.meta:')
print(czi.meta)
xpath_str = "./Metadata/Information/Document/CreationDate"
_creationdate = czi.meta.findall(xpath_str) # [<Element 'CreationDate' at 0x7fa670647f40>]
print('_creationdate:', _creationdate)
for creationdate in _creationdate:
# xml.etree.ElementTree.Element
print(' creationdate:', creationdate)
print(dir(creationdate))
_datetime = creationdate.text
cellpose.io.add_model
-
[done] Add histogram widget. Re-use histogram from PyMapManager
-
Add 'accept' column to napari-layer-table. This will be the start of editing from the table!
-
If point is selected and user hits keyboard 'a' then toggle 'accept' True/False
-
emit signal with point and row dict (including 'accept' column)
-
[done] swap in my table/model from napari-layer-table
-
hide lots of columns
-
make sure copy of table copies all columns
-
[done] make oligoAnalysis a package
-
make oligoanalysis a napari plugin
-
[done] make dark interface with qdarkstyle (see pymapmanager)
-
[done] reduce font size (see pymapmanager)
-
fix contrast slider signal/slot when oligointerface gets slot contrast changed, check selected layer name and that it is an image layer and directly call layer.contrast_limits = [min, max]
-
when making oligoanalysis dataframe, pass entire df (all columns) and use hide() api to hide columns. goal is to get copy() to copy entire dataframe
-
in napari viewer, on edit 'accept', actually set oligo analysis label df
-
[done] on file selection, set gaussian sigma
-
implement 'set folder'
-
expand loaded file types. Right now we only do czi. Whatever we load, we need to know the number of channels
-
[done] in napari-layer-table, add api to set font size
-
[hard] if we have a cellpose model, run the model of merged rgb
-
rename repo to 'dapi-ring-analysis'. This is more general purpose than oligo
- Need to switch my naming of channels. Use 'DAPI' and 'CYTO' instead of 'green' and 'red'?
Package Version
----------------------------- -----------
aicsimageio 4.9.2
aicspylibczi 3.0.5
alabaster 0.7.12
anyio 3.6.2
appdirs 1.4.4
appnope 0.1.3
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
asciitree 0.3.3
asttokens 2.1.0
attrs 22.1.0
Babel 2.10.3
backcall 0.2.0
beautifulsoup4 4.11.1
bleach 5.0.1
build 0.9.0
cachetools 5.2.0
cachey 0.2.1
cellpose 2.1.0
certifi 2022.9.24
cffi 1.15.1
charset-normalizer 2.1.1
click 8.1.3
cloudpickle 2.2.0
commonmark 0.9.1
dask 2022.10.2
debugpy 1.6.3
decorator 5.1.1
defusedxml 0.7.1
dnspython 2.2.1
docstring-parser 0.15
docutils 0.19
elementpath 2.5.3
email-validator 1.3.0
entrypoints 0.4
executing 1.2.0
fasteners 0.18
fastjsonschema 2.16.2
fastremap 1.13.3
freetype-py 2.3.0
fsspec 2022.10.0
google-api-core 2.10.2
google-auth 2.14.0
google-cloud-core 2.3.2
google-cloud-storage 2.5.0
google-crc32c 1.5.0
google-resumable-media 2.4.0
googleapis-common-protos 1.56.4
HeapDict 1.0.1
hsluv 5.0.3
idna 3.4
imagecodecs 2022.9.26
imageio 2.22.3
imagesize 1.4.1
importlib-metadata 5.0.0
importlib-resources 5.10.0
ipykernel 6.17.0
ipython 8.6.0
ipython-genutils 0.2.0
ipywidgets 8.0.2
jedi 0.18.1
Jinja2 3.1.2
jsonschema 4.16.0
jupyter 1.0.0
jupyter_client 7.4.4
jupyter-console 6.4.4
jupyter_core 4.11.2
jupyter-server 1.21.0
jupyterlab-pygments 0.2.2
jupyterlab-widgets 3.0.3
kiwisolver 1.4.4
llvmlite 0.39.1
locket 1.0.0
lxml 4.9.1
magicgui 0.6.0
MarkupSafe 2.1.1
matplotlib-inline 0.1.6
mistune 2.0.4
napari 0.4.16
napari-console 0.0.6
napari-layer-table 0.0.10
napari-plugin-engine 0.2.0
napari-svg 0.1.6
natsort 8.2.0
nbclassic 0.4.7
nbclient 0.7.0
nbconvert 7.2.3
nbformat 5.7.0
nest-asyncio 1.5.6
networkx 2.8.7
notebook 6.5.2
notebook_shim 0.2.0
npe2 0.6.1
numba 0.56.3
numcodecs 0.10.2
numpy 1.23.4
numpydoc 1.5.0
ome-types 0.3.1
opencv-python-headless 4.6.0.66
packaging 21.3
pandas 1.5.1
pandocfilters 1.5.0
parso 0.8.3
partd 1.3.0
pep517 0.13.0
pexpect 4.8.0
pickleshare 0.7.5
Pillow 9.3.0
Pint 0.20.1
pip 22.3
pkgutil_resolve_name 1.3.10
plotly 5.11.0
prometheus-client 0.15.0
prompt-toolkit 3.0.31
protobuf 4.21.9
psutil 5.9.3
psygnal 0.6.0
ptyprocess 0.7.0
pure-eval 0.2.2
pyasn1 0.4.8
pyasn1-modules 0.2.8
pycparser 2.21
pydantic 1.10.2
Pygments 2.13.0
PyOpenGL 3.1.6
pyparsing 3.0.9
PyQt5 5.15.7
PyQt5-Qt5 5.15.2
PyQt5-sip 12.11.0
pyqtgraph 0.13.1
pyrsistent 0.19.1
python-dateutil 2.8.2
pytomlpp 1.0.11
pytz 2022.5
PyWavelets 1.4.1
PyYAML 6.0
pyzmq 24.0.1
qtconsole 5.3.2
QtPy 2.2.1
requests 2.28.1
resource-backed-dask-array 0.1.0
rich 12.6.0
rsa 4.9
scikit-image 0.19.3
scipy 1.9.3
Send2Trash 1.8.0
setuptools 65.5.0
six 1.16.0
sniffio 1.3.0
snowballstemmer 2.2.0
soupsieve 2.3.2.post1
Sphinx 5.3.0
sphinxcontrib-applehelp 1.0.2
sphinxcontrib-devhelp 1.0.2
sphinxcontrib-htmlhelp 2.0.0
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 1.0.3
sphinxcontrib-serializinghtml 1.1.5
stack-data 0.6.0
superqt 0.3.8
tenacity 8.1.0
terminado 0.17.0
tifffile 2022.10.10
tinycss2 1.2.1
tomli 2.0.1
toolz 0.12.0
torch 1.13.0
tornado 6.2
tqdm 4.64.1
traitlets 5.5.0
typer 0.6.1
typing_extensions 4.4.0
urllib3 1.26.12
vispy 0.10.0
wcwidth 0.2.5
webencodings 0.5.1
websocket-client 1.4.1
wheel 0.37.1
widgetsnbextension 4.0.3
wrapt 1.14.1
xarray 2022.10.0
xmlschema 1.11.3
zarr 2.13.3
zipp 3.10.0