Qin Yu qin-yu

Bioimaging Data Management: Tools, Platforms and Resources

Summarised from the EMBL-EBI Imaging Data Stewardship Workshop at MRC LMB (2026)

Training, Community & Resources

BioImagingUK Training GitHub
EBI Training Events (data management courses)
- Data management in a bioimage informatics data flow
Principles of research data management

Installation instruction for the `cvapipe_analysis` software

cd to the folder where you put folders of your softwares
download the repository by git clone https://github.com/AllenCell/cvapipe_analysis.git
- If you don't know git please check out my tutorial: How to configure Git and setup GitHub on new machine
go into the downloaded repo cd cvapipe_analysis
use the publication version of the code git checkout tags/nature-paper
create a new Conda environment conda create --name cvapipe python=3.8 and activate it conda activate cvapipe
- If you don't know conda please check out my documentation: Install Mamba
install the downloaded code pip install -e .

When you are not able to embed/add an image from GitHub to your MarkDown files such as a page in Sphinx or Jupyter Book, maybe you are using blob instead of raw in the image URL.

For example, if you use https://github.com/hci-unihd/plant-seg/raw/assets/images/plantseg_overview.png then the link is to an image, but https://github.com/hci-unihd/plant-seg/blob/assets/images/plantseg_overview.png is to the GitHub page that contains the image.

Click to see the difference:

Upload Package to PyPI and Conda

Publishing to PyPI Manually
- Resources
- Workflow
Contributing to Conda Manually
- Resources
- Workflow

Publishing to PyPI Manually

If Chrome browser doesn't show correct resolution and sharp boundaries, append this parameters /high-dpi-support=1 /force-device-scale-factor=1 to the target field in Properties:

For easily merging some labels in an instance segmentation mask:

Paintera: https://github.com/saalfeldlab/paintera
bigCAT: https://github.com/saalfeldlab/bigcat
webKnossos: https://github.com/scalableminds/webknossos
Napari: https://github.com/napari/napari

Ubuntu20.04 Wine 6.0 微信中文显示方块/方框

如果希望在Ubuntu使用Windows版微信：

安装 Wine sudo apt-get install wine

先把环境改了省事：

$ export WINEARCH=win32
$ export WINEPREFIX=/home/qinyu/Wine/WeChat

创建 Wine Bottle

If conda install fails to resolve dependencies, install packages with all channels used before. For example, use

$ conda install napari vigra elf nifty pytorch torchvision torchaudio cudatoolkit=11.1 -c pytorch -c nvidia -c conda-forge -c cpape

instead of

$ conda install napari vigra nifty -c conda-forge

If you have GSettings schema undefined not found during installation of Panel World Clock (Lite) by Nei, then it might not be a problem with GSettings or gnome. If you installed gnome-clock with snap, remove it by snap remove gnome-clock and then reinstall it by apt. Now reinstall panel world clock, logout and login again.

	import os
	import re
	import subprocess
	from datetime import datetime, timedelta


	def set_creation_date(file_path, creation_date):
	"""
	Set the creation date of a file.