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Add prototype for OME-ZARR export #87

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Features

  • Supports multichannel data export
  • Adds metadata output both as separate .txt metadata file and internal OME-ZARR metadata table (using the NGIO backend)

Notes

  • Multi-tile dataset acqusition has not been tested! Current implementation likely does not handle tiled acquisitions correctly.
  • For reading and interacting with the resulting OME-ZARR data and metadata tables, I recommend using the ngio library.

nvladimus and others added 30 commits June 17, 2024 17:18
@nvladimus
dirty and non-working script attempt
47e79fd
@nvladimus
basic timelapse script works, but no way to stop after N time points …
df63cd9 
…reached.
@nvladimus
increase exposure limits
e1c3e05
@nvladimus
Merge branch 'master' of https://github.com/mesoSPIM/mesoSPIM-control
5420eea
@nvladimus
change logging to thread name instead of ID
7e77155
@nvladimus
remove random noise from simulated image for speed (500 ms-> 50 ms)
37df42d
@nvladimus
major: moved ImageWriter to separate thread
98d4c16
@nvladimus
port to python 3.12, add garbage collection
06e0785
@nvladimus
create basic TIFF writing speed test
ee4d404
@nvladimus
major: changed sharing data between camera and writer for deque in…
d106a3b 
…stead of signal/slot
@nvladimus
revert mesoSPIM_State.py, cleanup
81a3a15
@nvladimus
pre-release cleanup
66a5e05
@nvladimus
update framerates to measured values
0e0d341
@nvladimus
stop the acquisition in a thread-safe way, with signal/slot
46bb6e0
@nvladimus
update dependencies to the latest (py3.7), except PyQt5 (avoid StateO…
882c987 
…bject deleted issues)
@nvladimus
lower the camera and writer thread priorities
7d7a2b9
@nvladimus
reverse PyQt5-sip upgrade
9dde301
@nvladimus
reverse upgrade qdarkstyle
8c16d17
@nvladimus
Migrate to py 3.12.
88f15df 
- make State() singleton compatible with py 3.12
- show an image every 'camera_display_temporal_subsampling frames' timepoint
-update README to use Mamba
@nvladimus
version bump and comments
8dac7a4 
adjust expected framerate

cleanup
@nvladimus
change position timer period, update CHANGELOG and cleanup
0e35e8a
@nvladimus
debug message min and max values for DAQ error out-of-range troublesh…
8e2eba4 
…ooting
@nvladimus
roll back ASI polling int to 250 ms
57ccf90
@nvladimus
Revert "danger: potentially slow acquisitions, move_relative(... wait…
33ab196 
…_until_done=True), direct call instead of signal."

This reverts commit 659332d.
@nvladimus
clean up
5366148
@nvladimus
Update README.md
d62960e
@nvladimus
Update pyproject.toml
764107a
@nvladimus
Merge branch 'release/candidate-py312' of https://github.com/mesoSPIM…
7b71906 
…/mesoSPIM-control into release/candidate-py312
@TchLenn
UCL 5-colour config file
144a583
@TchLenn
no signals to shutter_left
2ccd607
nvladimus and others added 30 commits February 25, 2025 12:24
@nvladimus
breaking: move image updates to deque
218a820
@nvladimus
remove deprecated subsampling of displayed images
1db0392
@nvladimus
bugfix: explicit initialization of first raw in Acq Manager
fcf6ee5
@nvladimus
Update CHANGELOG.md
591ba2c
@nvladimus
fix the AF function
528a113 
cleanup
@nvladimus
safety UI for zoom change
93fe10b
@nvladimus
disable feedback from camera to GUI, to avoid looping
ad99ff8
@nvladimus
disable unnecessary sig_update_gui_from_state to avoid feedback loops
8993af2
@nvladimus
example file of exposure scaling
8059e5c
@nvladimus
restore screen subsampling
d633744
@nvladimus
fix LS markers and crosshairs positions
3a0f028
@nvladimus
fix interactive subsampling ratios
b666f49
@nvladimus
fix Box ROI
cfa0363
@nvladimus
Update mesoSPIM_MainWindow.ui
ce54b7a
@nvladimus
add user forum link and static badge
512472e
@nvladimus
Section rename (Further resources)
b048ffb
@nvladimus
test new docs format
e46466f
@nvladimus
add CPU core id to debug info
aad7cd5
@nvladimus
clean up
f23f760
@nvladimus
breaking change? Serial worker moved to Core thread.
6f7a7f3
@nvladimus
major: return of temporal subsampling, minimize status messages, proc…
ffe58b2 
…ess all events
@nvladimus
minor fix
ea63c35
@nvladimus
Create config_HIFO-H45-PFI0-direct-connection.py
acb8f85
@nvladimus
Merge branch 'release/candidate-py312'
a475d5b
@nvladimus
Update CHANGELOG.md
881987c
@nvladimus
version bump to 1.11.1
85f4807
@severinothomasin
implemented prototype for ome zarr export (multichannel is supported,…
fa7da41 
… multi-tile and metadata table handling not yet)
@severinothomasin
Added support for metadata handling
94bfa2d
@nvladimus
revert [fa7da41] to remove linux functions
1604a00
@nvladimus
add necessary changes from [fa7da41]
727e66e
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3 participants

@severinothomasin @nvladimus @TchLenn