Feat/add technologies

[dannda]

• Add processing functions for Xenium and MERSCOPE (already included in the notebooks) to the pipeline scripts.
• Add the optional prefix parameter to the data parameters file, so output filenames are prefixed {project}-{dataset}-{prefix}-file.ext.
• Add data type raw_image_data to generate/pre-process raw images. Needed for MERSCOPE output raw images are they are split by channel to different tif images. merscope_raw function in process_merscope.py then handles concatenating the channels to a single tif image that can then be processed by Process_images.
• Add support for multiple image output from raw_image_data and label_image_data. If data produces multiple images, processing scripts should append an additional prefix so images are not overwritten.
• Process that converts images to zarr directly uses images filenames if they come from raw_image_data or label_image_data as to not loose any prefixes.

[codecov-commenter]

Codecov Report

Patch coverage: 41.23% and project coverage change: -4.46 :warning:

Comparison is base (1764504) 49.65% compared to head (9747816) 45.20%.

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Additional details and impacted files

```diff @@ Coverage Diff @@ ## dev #61 +/- ## ========================================== - Coverage 49.65% 45.20% -4.46% ========================================== Files 10 12 +2 Lines 439 573 +134 ========================================== + Hits 218 259 +41 - Misses 221 314 +93 ``` | [Impacted Files](https://codecov.io/gh/haniffalab/vitessce-pipeline/pull/61?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab) | Coverage Δ | | |---|---|---| | [bin/build\_config.py](https://codecov.io/gh/haniffalab/vitessce-pipeline/pull/61?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab#diff-YmluL2J1aWxkX2NvbmZpZy5weQ==) | `0.00% <0.00%> (ø)` | | | [bin/process\_merscope.py](https://codecov.io/gh/haniffalab/vitessce-pipeline/pull/61?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab#diff-YmluL3Byb2Nlc3NfbWVyc2NvcGUucHk=) | `23.68% <23.68%> (ø)` | | | [bin/process\_xenium.py](https://codecov.io/gh/haniffalab/vitessce-pipeline/pull/61?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab#diff-YmluL3Byb2Nlc3NfeGVuaXVtLnB5) | `34.78% <34.78%> (ø)` | | | [bin/consolidate\_md.py](https://codecov.io/gh/haniffalab/vitessce-pipeline/pull/61?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab#diff-YmluL2NvbnNvbGlkYXRlX21kLnB5) | `92.85% <50.00%> (ø)` | | | [bin/generate\_image.py](https://codecov.io/gh/haniffalab/vitessce-pipeline/pull/61?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab#diff-YmluL2dlbmVyYXRlX2ltYWdlLnB5) | `58.33% <58.33%> (ø)` | | | [bin/router.py](https://codecov.io/gh/haniffalab/vitessce-pipeline/pull/61?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab#diff-YmluL3JvdXRlci5weQ==) | `83.33% <62.50%> (-5.56%)` | :arrow_down: | | [bin/process\_spaceranger.py](https://codecov.io/gh/haniffalab/vitessce-pipeline/pull/61?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab#diff-YmluL3Byb2Nlc3Nfc3BhY2VyYW5nZXIucHk=) | `61.40% <70.27%> (+28.07%)` | :arrow_up: | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=haniffalab)

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[dannda]

Notes on docker image:

• previous image based on bioformats2raw:0.4.0 is based on ubuntu 18 which caused issues when using pyvips to save a tif image with page-height (used when processing MERSCOPE raw image data) as it required libvips > 8.10 which has no builds for that ubuntu version
• changed image to be based on python:3.9 (debian 11). Building image requires platform to be amd64 for java libraries for bioformats2raw to work