Welcome & Guide
Welcome to the imzML_Writer documentation page!
imzML_Writer is available as:
(Recommended) A distributable package on pypi (for CLI, stable GUI,
pip install imzML-Writer).(Experimental) A simple standalone executable on both Mac and PC (.app and .exe respectively).*
*: Both imzML Writer and Scout are available on Mac, but only Writer is available on PC at this time.
Compatibility
Many imzML file readers are available both commercially and as open-source software. Of the popular software we’ve tested, file compatible for imzML’s generated with imzML_Writer are:
Software |
Functioning |
Comments |
|---|---|---|
Yes |
||
Yes |
||
Yes |
||
Yes |
||
Yes |
||
Yes |
Pixels must be written as integers for automatic read-in (can specify manually) |
|
Yes |
If you find need files to work with a particular software, or if you’d like to report additional software that imzML_Writer is compatible with please don’t hesitate to reach out.
Installation
MS Convert
For both versions, imzML Writer relies on MS convert to convert raw instrument data into the open format mzML, requiring a working install.
On PC, download the latest msconvert release from ProteoWizard and navigate through the installer. If you want to run msconvert from the command line, make sure that msconvert is added to the system PATH, either during installation or by following the instructions here.
For use with imzML Writer, you can skip this step and will instead be prompted to search (automatically or manually) for msconvert’s install location the first time you go to convert files:
On Mac, download Docker and open up the GUI dashboard. You will be prompted to install the docker image for msconvert the first time you try to convert some raw files:
Note that this may take several minutes to download/install. If this isn’t working, you can manually download the docker image by opening the Terminal app and running the command:
docker pull chambm/pwiz-skyline-i-agree-to-the-vendor-licenses
You can verify successful install in the Docker dashboard under the images tab:
Python package
Running imzML Writer from the python package is the recommended option for most users, allowing for both stable GUI use and a command line interface (CLI) for batch processing.
To install, make sure you have Docker (Mac) or MSconvert (PC) installed as above. Then, in your python environment run:
pip install imzML-Writer
Once active, you can easily launch the GUI by creating a python example.py with contents:
import imzml_writer.imzML_Writer as iw
iw.gui()
Then run the script (python example.py) to launch the GUI. If you already have some imzML files and just want to view them with the scout, restructure example.py:
import imzml_writer.imzML_Scout as scout
##Call with no arguments opens it empty and you can use the GUI to search for your file
scout.main()
##Call with full or relative pathing to the imzML will open the specified file
path_to_imzML = "/Example/File/path/my_image.imzML"
scout.main(path_to_imzML)
This covers the basic GUI functionality, for further details on running the CLI see the documentation pages.
Standalone apps
Mac
Download the App Bundle from Github and grab the Mac distribution.
Move the imzML_Writer.app file into your Applications folder (Note: This step is required). Then double-click the .app bundle to launch the application. Depending on your security settings, Apple may block the launch with the following pop-up:
If so, click ok (*not move to trash*), navigate to your security settings (System Settings --> Privacy & Security), scroll to the bottom, and click “open anyways” for imzML_Writer.
This should launch the UI and the application is ready for typical operation.
PC
Download the PC distribution from the Github release, move the entire PC executable folder (imzML_Writer.exe, obo folder, & _internal folder) and place it somewhere convenient on your PC.
Then, open the folder and launch imzML Writer by double-clicking imzML_Writer.exe. This will launch a terminal window and the GUI. Provided msconvert is installed and added to the path, you should be good to go!
Table of Contents