czinspect currently extracts data from a .czi file using the directory segments for subblocks and attachments. In the same vein as #5, it might be useful to process subblocks using the segment-local metadata in the case of file corruption.

extractjxr supports dumping a .czi file's metadata to a file (currently using a shoddy, hand-rolled JSON formatter), which a gives a human readable and pre-prepared representation of the file's metadata. czinspect should implement this (or something similar) to attain feature parity.

czinspect does not yet support subsampling ratio scanning for .czi files, which is required both as an informational feature and for filtering certain levels of the stored image pyramid when extracting image tiles.

Additionally, it is desirable for czinspect to be able to automatically guess the nearest subsampling level if given a level which does not exist in the file, so that a number of images can be extracted in bulk without having to scan all of them and set appropriate filter levels.

The CI builds for czinspect on macOS fail when creating the object files for the help files, due to the linker not recognising the flags in use. macOS also uses the Mach-O executable format instead of ELF, so the help text handling may need completely rewritten.

The ability to perform a sanity check of the metadata in a .czi file (i.e. that the metadata held in the ZISRAWDIRECTORY segment and the ZISRAWSUBBLOCK segments matches) would be a useful feature for troubleshooting issues in extracting images from the file.

czinspect has two forms of dynamic data structure, the lzstring and the lzbuf; the former implements dynamically allocated null-terminated strings and the latter implements dynamically allocated array of a given type. Internally these are implemented as macros over the same family of functions and structures. However, all that the underlying structure keeps track of is a pointer to an area on the heap and the length of this area; there is no mechanism for tracking how much of this area is in use. This causes issues when passing these structures (or pointers to them) through several different functions when used as array, as the length must be passed separately.

lzstring and lzbuf have different purposes, therefore their implementations should probably be seperate.

A cursory test of czinspect on an OpenBSD/macppc system shows that the big endian compatibility code does not function correctly. This problem has not yet been investigated in depth.

There are potential use cases where extracting only a few specific tiles from a .czi file would be desirable, such as inspecting image regions which cross tile edges. An external tool could examine dumped metadata (see #4), calculate the required tiles and then execute czinspect to extract only those tiles.

czinspect currently extracts tiles from an image in serial order; on systems with multiple cores and high-throughput I/O, extraction speed may be increased by extracting several tiles from an image file at once.

The image format used by tiles in a .czi file is usually JPEG-XR, which is unwieldy for a lot of applications as the image format is not common, which necessitates format conversion. Adding support for czinspect to do this in-line after extraction would remove the need for external tooling to do this after the fact.

The proposed model is to extract a JXR image tile and then fork+exec JxrDecApp from jxrlib to convert to TIFF. Further conversions could then be performed with other programs such as vips or ImageMagick's convert.