A Python module and CLI tool for converting proprietary microscopy formats to TIFF with JSON metadata sidecar files.
Both supported modules and modules working with errata are listed below.
| Sensor | Status | Errata/Notes |
|---|---|---|
| Imaging FlowCytobot/IFCB (.adc, .hdr, .roi) | ✅ | |
| LISST-Holo (.pgm) | ✅ | Only extracts raw interference field, does not reconstruct images. Metadata export broken. |
| LISST-Holo2 (.pgm) | ✅ | See above |
| FlowCam | ❌ | In active development |
- pillow
- numpy
- holopy (for LISST-Holo/LISST-Holo2 "construct" mode only)
- xarray
- h5netcdf
- nose
- matplotlib
- h5py
- pyYaml
- scipy
- imp
For essential dependencies you can use the following command:
$ pip install pillow numpy
HoloPy is not avaliaiable via PIP. If you are using anaconda, you may install it there. Alternatively, install from source by following instructions at https://holopy.readthedocs.io/en/master/tutorial/dev_tutorial.html. Alternatively, use the install script at scripts/install-holopy.sh
This library is comprised of work from various researchers.
LISST-Holo decoder based on work by Sari Giering, Will Major and Mojtaba Masoudi