Image Data Analysis
The MIC offers to the imaging community support for all questions related to digital image processing. You are not sure how to process your imaging data? You have a script that doesn't work properly? You want to discuss a project? Just send an email to our bioimage analyst Guillaume Witz and he will get back to you. To learn more about the service, continue reading below!
The MIC support for image processing is provided via an agreeement with the Data Science Lab (DSL), a core facility of the university. DSL provides support for all members of the university but the agreement with the MIC guarantees a free dedicated support for bioimage analysis related questions with an expert in the field. You can find below a list of the type of services that are provided for free as well as an explanation of how DSL can directly help you for larger projects. In addition, DSL provides the MIC with regular trainings for software usage and programming. If you would like to learn about a software or method not yet covered, let us know and we might organise a dedicated training.
Free MIC-DSL service
You can consult with the MIC-DSL support on a variety of topics. For example:
- Software and hardware consulting: you are not sure which software to use to analyze your data, or don't know how to run your analysis on a computing cluster
- Debugging: you developed or received a script to automate a data processing workflow but it doesn't work as expected
- Project consulting: you are writing an grant application that includes complex data analysis and would like to discuss how to correctly formulate it
- Computing: DSL manges a computer station of the MIC dedicated to image processing. Common image processing software are installed on this computer and you can request custom installations if needed. The computer, located at the TKI, has 8 cores, 128GB of RAM and an NVIDIA Quadro P4000 graphics card, which makes it an ideal tool for processing and visualising large imaging datasets. Get in touch with Guillaume Witz to organise bookings
- Commercial software: DSL manages for the MIC a server providing access to the commerical software Imaris. Labs can participate in our Imaris program for a fee (around 1200CHF/year) and get access to the server on their own computers. If you have interest in other commercial software, we can organise demonstrations or put you in contact with other users.
The MIC-DSL typically provides support for a series of common image processing software such as Fiji, CellProfiler, Ilastik, Python, R etc. If you want to use some more specialized software you can still reach out to us and we will attempt to put you in contact with other MIC or DSL members experts.
Larger scale projects are not included in the MIC-DSL agreement but DSL can still help you! Such projects typically involve the development of custom software or setting up IT infrastructure. After initial free consulting discussions, work on such projects is covered by separate agreements directly between DSL and labs or institutes. These agreements contain clear deliverables as well as funding solutions either in personal employment points or direct fund transfers. Note that you can also include DSL in early stages of grant writing so that data handling and processing is appropriately planned and funded.
Examples of questions you might have
- Where should I store my data?
- What software should I use to visualize my 3D time-lapse data?
- How can I customize Fiji using a script?
- Does my CellProfiler pipeline make sense?
- How can I get the necessary computing power to process my hundreds of Gb of data?
- I need custom image processing for a new type of data. Can someone help?
- I can’t open my data, connect to a server, run a Fiji plugin, etc. I need help!
- Where can I learn to do some of the above things myself?
Tools and Services
- Beginner Image Processing with Python course
Github repository with all the material for a beginner course in image processing with Python
- Data analysis and visualization with Python: Course content for a course regularly given in the frame of the Transferable Skills program
- Deep Learning with PyTorch for computer vision: introductory course on PyTorch for computer vision
- Python Pandas course
You want to learn how to efficiently handle multiple table outputs of Fiji or CellProfiler to make plots? This course will walk you through the Pandas package which is designed to handle tabular formats in Python. Basic and more advanced plotting examples are also given.
- Fiji basics course
Fiji (ImageJ) is the go-to tool if you quickly want to have a look at your imaging data and perform basic image processing. These are the slides used for the MIC course for Fiji beginners. If you follow them and try some of the exercises, you should have a good overview of basic Fiji usage.
- Image processing station
The MIC has acquired a powerful image processing station which is made available to the imaging community. The station, located at TKI, has 8 cores, 128GB of RAM and an NVIDIA Quadro P4000 graphics card, which makes it an ideal tool for processing and visualising large imaging datasets. The commercial software Imaris as well as standard open-source software such as Fiji are available on the station and additional software can be installed upon request. Any research group can ask for access to the computer either to test software, e.g. in planning the purchase of a station, or for projects requiring only occasionally high computing power. Access requests should be addressed directly to Guillaume Witz who will evaluate them and offer support to users.