I believe there are 3 mainly options for this case:
- use microfluidic devices that are made to be reusable;
- use microfluidic devices that are not are not meant to be reusable but cheaper;
- devise a protocol of gentle cleaning.
The main options for devices made to be reusable are
- silicon;
- glass;
- low temperature co-fired ceramics (LTCC).
The main options for disposable devices are
- thermosets;
- hydrogel;
- thermoplastics;
- paper;
- elastomer (includes PDMS, which is the most commom elastoemr used in microfluidics).[1]
Which one to choose depends on your constraints of use and price. And price depends on if you can fabricate your devices or if you intend to buy it.
For imaging, probably the glass devices, which you already use, are the best choice. If you don't want to buy them, it is possible to do them, but the lack of characterisation might affect your reproducibility (about fabrication in [2]). If you are in a multidisciplinar research center there should be a microfluidics laboratory that can help you to make it, but it can take time and distract you from the focus of your research.
That said, maybe the best option is to learn a way to clean it gently. I don`t know if it can be done with with your particular device, but you can try some ideas from this document from Sigma-Aldrich for cleaning glassware: https://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Aldrich/Bulletin/al_techbull_al228.pdf
[1] Materials for Microfluidic Chip Fabrication Kangning Ren, Jianhua Zhou, and Hongkai Wu. Accounts of Chemical Research 2013 46 (11), 2396-2406 doi: 10.1021/ar300314s
[2] Iliescu C, Taylor H, Avram M, Miao J, Franssila S. A practical guide for the fabrication of microfluidic devices using glass and silicon. Biomicrofluidics. 2012;6(1):016505-016505-16. doi:10.1063/1.3689939.
