Note
Go to the end to download the full example code.
Single-FOV OME-Zarr#
This script shows how to create a single-FOV, single-scale OME-Zarr dataset, read data in read-only mode, append an extra time point to an existing dataset, and adding a new channel to an existing dataset.
import os
from tempfile import TemporaryDirectory
import numpy as np
from iohub.ngff import open_ome_zarr
Set storage path
tmp_dir = TemporaryDirectory()
store_path = os.path.join(tmp_dir.name, "ome.zarr")
print("Zarr store path", store_path)
Zarr store path /tmp/tmpvz_p5l5k/ome.zarr
Write 5D data to a new Zarr store
tczyx = np.random.randint(
0, np.iinfo(np.uint16).max, size=(5, 2, 3, 32, 32), dtype=np.uint16
)
with open_ome_zarr(
store_path, layout="fov", mode="a", channel_names=["DAPI", "GFP"]
) as dataset:
dataset["img"] = tczyx
Opening in read-only mode prevents writing
with open_ome_zarr(store_path, layout="auto", mode="r") as dataset:
img = dataset["img"]
print(img)
print(img.numpy())
try:
img[0, 0, 0, 0, 0] = 0
except Exception as e:
print(f"Writing was rejected: {e}")
<iohub.ngff.nodes.ImageArray '/img' (5, 2, 3, 32, 32) uint16 read-only>
[[[[[ 5186 19747 15752 ... 10938 34438 2138]
[39471 57729 24985 ... 30335 46497 32430]
[ 7219 48628 6437 ... 23778 6914 13166]
...
[26667 34415 6755 ... 9154 31374 14077]
[52199 36585 53879 ... 13876 26527 38623]
[35717 40959 1256 ... 65389 14858 39872]]
[[32944 57140 33450 ... 63914 11061 11758]
[19625 9277 33178 ... 5041 17889 49778]
[51302 713 46521 ... 33092 27379 59172]
...
[35072 32246 40404 ... 37701 63719 3653]
[41335 47060 8566 ... 12502 17842 34058]
[43097 39697 10227 ... 976 37421 51051]]
[[55767 22267 50282 ... 31564 16323 55264]
[50551 40308 64912 ... 57190 20954 54092]
[33407 16546 51943 ... 21316 25941 5595]
...
[46780 59486 35242 ... 16686 30974 10701]
[28260 4021 30699 ... 31163 60332 22292]
[50143 27158 29290 ... 60717 34252 15150]]]
[[[16822 21300 63525 ... 32727 55616 5704]
[41721 5631 17659 ... 53283 43385 13992]
[16503 42469 50535 ... 55833 36975 33466]
...
[49994 11938 9975 ... 29521 36577 25236]
[60987 1839 39393 ... 9062 39603 2044]
[ 62 8558 28163 ... 9948 50044 56551]]
[[21123 35207 32062 ... 23384 24571 5051]
[44078 6846 21994 ... 25097 6142 7422]
[37991 52282 47603 ... 35575 39885 25999]
...
[36827 54110 5255 ... 7205 16994 24598]
[12311 64206 17335 ... 39195 28482 33645]
[15534 51811 27215 ... 48267 24383 24940]]
[[65300 3430 11051 ... 3962 12928 42837]
[48259 43976 24460 ... 56132 34241 10815]
[42766 39439 44932 ... 50630 30857 45211]
...
[ 9923 36783 64989 ... 53106 52035 63423]
[63893 29752 11567 ... 53491 38310 51608]
[63013 2594 50930 ... 27030 7091 12027]]]]
[[[[23626 18753 36878 ... 44999 44717 11041]
[30806 8567 61489 ... 18490 24803 33616]
[43741 1772 54369 ... 28571 30484 38400]
...
[ 3876 19560 16907 ... 43146 19017 37515]
[ 3909 47593 53653 ... 10967 51403 41677]
[52990 65315 44671 ... 56308 12823 21797]]
[[10519 21671 29842 ... 64680 22607 15078]
[61208 60532 37959 ... 14422 30499 11668]
[21938 47800 24265 ... 35277 54981 35115]
...
[50914 50532 21742 ... 6343 60997 21866]
[ 4873 36683 55516 ... 6622 59865 47966]
[58301 23465 49117 ... 58593 62068 3050]]
[[47288 48340 53406 ... 63945 50288 21265]
[50427 25239 16654 ... 25587 49553 39873]
[22968 45128 10145 ... 34845 64628 21396]
...
[13155 41505 12395 ... 15180 14815 14242]
[ 6930 21234 14063 ... 10120 10927 53993]
[22749 48280 6785 ... 8711 45709 43286]]]
[[[49676 65531 21922 ... 30189 63863 22023]
[54009 30671 18206 ... 36632 50949 49630]
[22223 1296 64602 ... 45803 34872 34374]
...
[50200 12591 15234 ... 20787 8977 26381]
[62850 19375 12347 ... 19549 11021 6109]
[53804 25089 22475 ... 4321 32712 60951]]
[[27624 5448 8399 ... 56288 19839 5679]
[59668 56135 62146 ... 51077 63452 27317]
[20364 44773 62406 ... 11031 17637 32822]
...
[63651 29491 21182 ... 24036 50149 36025]
[63484 61590 23322 ... 29007 41873 31259]
[41936 44535 47258 ... 53199 24688 2028]]
[[44441 51874 29188 ... 56544 14441 29240]
[10816 22996 28071 ... 10234 8246 48523]
[17391 30084 58196 ... 6044 35676 1071]
...
[ 1867 6521 6043 ... 7506 1917 19639]
[19358 35833 46393 ... 15452 7940 47845]
[50834 32641 16014 ... 6412 40053 54290]]]]
[[[[31908 9296 47483 ... 17317 13231 31019]
[26644 7249 33247 ... 39852 2368 62921]
[ 5679 16264 63462 ... 57238 47553 31702]
...
[20993 60459 57235 ... 40356 13478 43830]
[46882 51281 43989 ... 7912 1229 39715]
[28840 1835 31633 ... 29482 58519 14640]]
[[43335 62506 21574 ... 59122 15056 7385]
[45221 41407 57799 ... 54850 54 41612]
[13604 37654 24565 ... 32666 16526 50661]
...
[54275 56488 38591 ... 59975 51999 61105]
[19166 25071 47566 ... 27708 45375 51324]
[27752 39805 21575 ... 15165 63329 114]]
[[14078 13602 3768 ... 955 61635 55717]
[23461 45178 63505 ... 22483 35352 20436]
[56414 35413 64256 ... 52880 50051 5647]
...
[50351 49687 31507 ... 37120 41182 48466]
[ 1186 55536 32137 ... 62219 37035 6869]
[24898 26572 1191 ... 31802 34642 8573]]]
[[[52768 30444 17675 ... 45512 62861 30213]
[23990 11631 43841 ... 46769 30960 30882]
[64840 237 23736 ... 52221 28489 60239]
...
[59332 49815 54022 ... 63251 2673 41909]
[42672 47159 62151 ... 28987 29691 29885]
[52644 8196 33225 ... 28520 29959 17064]]
[[13166 9635 27840 ... 26162 52123 48495]
[58056 32403 37659 ... 26100 20351 24143]
[18112 36539 65149 ... 61748 27366 50889]
...
[33562 39205 109 ... 1829 18220 47414]
[57495 26035 35876 ... 9296 46677 1689]
[47605 54175 18941 ... 34930 51520 6617]]
[[57275 45090 18091 ... 19142 15756 15153]
[33324 57166 42362 ... 34846 64045 41889]
[60465 48092 57445 ... 39913 59066 6674]
...
[37776 19448 21487 ... 2781 56320 12893]
[64534 24329 11104 ... 47218 62373 53421]
[19071 57919 18160 ... 28220 55497 32316]]]]
[[[[37301 31472 35260 ... 54691 10075 3759]
[47146 55450 45071 ... 8290 59235 37554]
[22006 18950 12072 ... 22522 27526 544]
...
[42105 22099 52154 ... 49672 56858 62485]
[47870 13268 15436 ... 17472 5046 12398]
[41455 1663 26482 ... 35990 58117 28005]]
[[ 6147 30748 64182 ... 40837 60652 34662]
[13835 64984 31733 ... 32577 49209 43805]
[50958 16329 56543 ... 31507 41775 16920]
...
[44546 36052 41911 ... 46997 7097 45330]
[26551 40941 29351 ... 41914 1774 30331]
[42312 837 4408 ... 17382 17591 953]]
[[11970 33425 3448 ... 33304 18951 5468]
[51008 6032 20597 ... 27631 64688 21155]
[11499 308 54452 ... 7633 44071 57519]
...
[25872 30055 19648 ... 60901 35953 5721]
[64324 26041 11609 ... 10636 33565 47757]
[31818 17814 30132 ... 27169 62222 36587]]]
[[[45356 3154 34204 ... 33270 31580 59739]
[34290 44916 42791 ... 42908 20927 37872]
[38433 29397 46994 ... 48530 2579 25847]
...
[ 5242 24816 38506 ... 32001 21130 4287]
[23349 65107 16022 ... 1635 56936 6982]
[58020 34011 7903 ... 28644 49965 57722]]
[[13682 42508 11448 ... 37159 22510 11332]
[ 3156 20456 58148 ... 21725 46470 26853]
[12841 39681 50530 ... 35605 54832 30765]
...
[ 4662 39376 7778 ... 52888 62138 24314]
[39381 31512 40891 ... 59604 63767 60828]
[47263 43577 38697 ... 47337 45205 28234]]
[[54345 63808 21980 ... 41029 25517 61896]
[45049 39006 24089 ... 49449 27919 15703]
[25806 4857 53509 ... 13738 5024 51174]
...
[60093 22632 27177 ... 23309 62939 35213]
[42684 64264 20073 ... 43601 12612 12076]
[15172 65481 44181 ... 40619 34941 62467]]]]
[[[[35551 56409 31827 ... 58351 58463 64734]
[56340 17630 64400 ... 51665 20937 4177]
[36684 46808 32523 ... 63743 31573 40003]
...
[22636 20615 59250 ... 28279 47673 2068]
[18485 18471 34759 ... 7858 16662 39544]
[53983 53303 10083 ... 23720 60000 28432]]
[[37805 7763 58366 ... 19217 19260 58011]
[27766 55599 46769 ... 63871 28965 2032]
[56866 6712 18448 ... 54715 4493 55011]
...
[ 7126 34347 44261 ... 17528 3569 23086]
[46481 2019 19159 ... 59371 42118 51115]
[ 8012 56260 63004 ... 48127 2533 3454]]
[[ 5887 6797 20288 ... 44853 5813 53047]
[14105 33501 38104 ... 24359 44687 1199]
[17810 8124 52002 ... 3616 15414 32481]
...
[14634 26374 16130 ... 53780 35926 42107]
[25555 41946 4362 ... 31215 47669 4318]
[58123 42346 7374 ... 51001 1135 29380]]]
[[[ 449 13072 54085 ... 20857 13366 30686]
[60831 64410 10178 ... 62078 60698 27240]
[25948 49770 17283 ... 64310 5273 37470]
...
[45919 30825 28972 ... 45233 40068 9447]
[38679 61189 29979 ... 8808 61616 15013]
[17911 41139 49735 ... 7275 39554 11752]]
[[59865 37393 10874 ... 44521 51779 34386]
[60616 27312 33925 ... 46795 13534 26608]
[65088 51455 52224 ... 62881 48392 57791]
...
[27034 58269 11115 ... 42945 56026 52969]
[56221 29112 64780 ... 44690 2994 21791]
[39503 26843 58534 ... 13781 10486 9752]]
[[35563 51033 11811 ... 8665 24438 41828]
[33745 54505 3105 ... 41110 50362 27635]
[38089 20862 21625 ... 455 59255 37649]
...
[54398 35361 37893 ... 28155 35879 45541]
[51174 8948 54023 ... 45265 2196 62077]
[53225 54773 7226 ... 33550 44145 24246]]]]]
Writing was rejected: object is read-only
Append a new timepoint to an existing dataset
new_1czyx = np.random.randint(
0, np.iinfo(np.uint16).max, size=(1, 2, 3, 32, 32), dtype=np.uint16
)
with open_ome_zarr(store_path, layout="fov", mode="r+") as dataset:
img = dataset["img"]
print(img.shape)
img.append(new_1czyx, axis=0)
print(img.shape)
(5, 2, 3, 32, 32)
(6, 2, 3, 32, 32)
Modify channels
# Open the dataset used above
dataset = open_ome_zarr(store_path, mode="r+")
dataset.print_tree()
# Append a new channel and write a Z-stack
new_zyx = np.random.randint(
0, np.iinfo(np.uint16).max, size=(3, 32, 32), dtype=np.uint16
)
dataset.append_channel("New", resize_arrays=True)
dataset["img"][0, 2] = new_zyx
print(dataset.channel_names)
dataset.print_tree()
# Rename the new channel
dataset.rename_channel("New", "Renamed")
print(dataset.channel_names)
# Write new data to the channel
new_tzyx = np.random.randint(
0, np.iinfo(np.uint16).max, size=(6, 3, 32, 32), dtype=np.uint16
)
c_idx = dataset.get_channel_index("Renamed")
dataset["img"][:, c_idx] = new_tzyx
# Which is equivalent to:
if False: # remove this line
dataset.update_channel("Renamed", target="img", data=new_tzyx)
# Close the dataset
dataset.close()
/
└── img (6, 2, 3, 32, 32) uint16
['DAPI', 'GFP', 'New']
/
└── img (6, 3, 3, 32, 32) uint16
['DAPI', 'GFP', 'Renamed']
Try viewing the images with napari-ome-zarr
Clean up
tmp_dir.cleanup()