9:30 A – 11:10 P
Coding
- Reorganizing Image_Analysis Repository
- New folder for 2013 Cell Reports paper
- Major rewrite of LSM parsing code
- And 6 hours later:
LSMextract.m– Takes a .lsm file, extracts all z-positions and all stage-positions into multicolor images, and also saves a max-projection image for the Z-stack. Optionally allows user to specify a sub-range of Z for each channel and an aribtrary subset of the positions.LSMread.m– creates a Datas structure from an LSM file, needed for other .lsm processing functions.readLSMmatfile.m– Extract a matlab image file from a .lsm file using info from the Datas structure. This replacesread_planeT.m, much, much more cleaned up, removed a ton of unnecessary code. Not backwards compatible as we dramatically simplified the input and output options.LSM2image.m– Takes a Datas file or a filename.lsm, returns an image for a specified z-position and stage-position (defaults to chose the first of each). Called by LSMextract in saving the images as RGB tifs and in building the max projections.
- ImageAnalysis Repository updated. Remaining files could probably use sorting into subdirectories. Meanwhile, it’s nice to have this repo active again as well as better documented for my existing published ImageAnalysis stuff.
computer
- working out incorporating hand written notes.
Writing
- Working out stochastic to deterministic model derivation.
- LatexBible ‘official’ latex formatting reference.
