Error: Cannot create 192 parallel PSOCK nodes #94
Description
Describe the bug
I'm trying to config Vitessce using AnnDataWrapper() off single cell adata.zarr (habib17.processed.zarr from https://python-docs.vitessce.io/notebooks/widget_brain.html).
When I get to render the widget here is the error I get
# Render the Vitessce widget
vc$widget(theme = "light")
# Error: Cannot create 192 parallel PSOCK nodes. Each node needs one connection, but there are only 124 connections left out of the maximum 128 available on this R installationTo Reproduce
library(vitessceR)
library(vitessceAnalysisR)
library(Seurat)
# Download example dataset
url <- "https://cf.10xgenomics.com/samples/cell/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz"
save_dir <- file.path("~/objects/Wrapper_function_test/", "seurat")
dir.create(save_dir)
download.file(url, destfile = file.path(save_dir, "filtered_gene_bc_matrices.tar.gz"))
untar(file.path(save_dir, "filtered_gene_bc_matrices.tar.gz"), exdir = save_dir)
# Load example dataset
pbmc.data <- Read10X(data.dir = file.path(save_dir, "filtered_gene_bc_matrices", "hg19"))
# Process example dataset (run PCA and cluster)
pbmc <- CreateSeuratObject(counts = pbmc.data, project = "pbmc3k", min.cells = 3, min.features = 200)
pbmc[["percent.mt"]] <- PercentageFeatureSet(pbmc, pattern = "^MT-")
pbmc <- subset(pbmc, subset = nFeature_RNA > 200 & nFeature_RNA < 2500 & percent.mt < 5)
pbmc <- NormalizeData(pbmc, normalization.method = "LogNormalize", scale.factor = 10000)
pbmc <- FindVariableFeatures(pbmc, selection.method = "vst", nfeatures = 2000)
all.genes <- rownames(pbmc)
pbmc <- ScaleData(pbmc, features = all.genes)
pbmc <- RunPCA(pbmc, features = VariableFeatures(object = pbmc))
pbmc <- FindNeighbors(pbmc, dims = 1:10)
pbmc <- FindClusters(pbmc, resolution = 0.5)
pbmc <- ScaleData(pbmc, features = all.genes, do.center = FALSE)
adata_path <- file.path("~/objects/Wrapper_function_test", "seurat", "pbmc3k.h5ad.zarr")
vitessceAnalysisR::seurat_to_anndata_zarr(pbmc, adata_path) #it doesn't work sometimes Just load an .zarr object I got from py
import os
from os.path import join, isfile, isdir
from urllib.request import urlretrieve
from anndata import read_h5ad
import scanpy as sc
from vitessce import (
VitessceConfig,
Component as cm,
CoordinationType as ct,
AnnDataWrapper,
)
from vitessce.data_utils import (
optimize_adata,
VAR_CHUNK_SIZE,
)
adata_filepath = join("/~/objects", "habib17.processed.h5ad")
if not isfile(adata_filepath):
os.makedirs("~/objects", exist_ok=True)
urlretrieve('https://covid19.cog.sanger.ac.uk/habib17.processed.h5ad', adata_filepath)
adata = read_h5ad(adata_filepath)
top_dispersion = adata.var["dispersions_norm"][
sorted(
range(len(adata.var["dispersions_norm"])),
key=lambda k: adata.var["dispersions_norm"][k],
)[-51:][0]
]
adata.var["top_highly_variable"] = (
adata.var["dispersions_norm"] > top_dispersion
)
# Create a .zarr file off the adata
zarr_filepath = join("~/objects", "habib17.processed.zarr")
if not isdir(zarr_filepath):
adata = optimize_adata(
adata,
obs_cols=["CellType"],
obsm_keys=["X_umap"],
var_cols=["top_highly_variable"],
optimize_X=True,
)
adata.write_zarr(zarr_filepath, chunks=[adata.shape[0], VAR_CHUNK_SIZE])Back to R/VitessceR
adata_path <- "~objects/habib17.processed.zarr"
# Create Vitessce view config
vc <- VitessceConfig$new(schema_version = "1.0.16", name = "My config")
dataset <- vc$add_dataset("My dataset")$add_object(AnnDataWrapper$new(
adata_path=adata_path,
obs_set_paths = c("obs/CellType"),
obs_embedding_paths = c("obsm/X_umap"),
obs_embedding_names = c("UMAP"),
obs_feature_matrix_path = "X"
))
scatterplot <- vc$add_view(dataset, Component$SCATTERPLOT, mapping = "UMAP")
status <- vc$add_view(dataset, Component$STATUS)
desc <- vc$add_view(dataset, Component$DESCRIPTION)
desc <- desc$set_props(description = "habib17.processed")
genes <- vc$add_view(dataset, Component$FEATURE_LIST)
heatmap <- vc$add_view(dataset, Component$HEATMAP)
vc$link_views(
list(scatterplot, heatmap),
list(CoordinationType$FEATURE_VALUE_COLORMAP_RANGE),
list(c(0.0, 0.05))
)
vc$layout(hconcat(
vconcat(scatterplot, heatmap),
vconcat(genes, vconcat(desc, status))
))
# Render the Vitessce widget
vc$widget(theme = "light")Expected behavior
The widget to pop up with the plots I set to display
Screenshots
Environment:
R 4.3.1
Package Version
abind 1.4-8
alphahull 2.5
annotate 1.80.0
AnnotationDbi 1.64.1
AnnotationFilter 1.26.0
AnnotationHub 3.10.0
anytime 0.3.9
ape 5.7-1
aplot 0.2.2
ArchR 1.0.2
argparse 2.2.2
aroma.light 3.32.0
arrow 15.0.1
askpass 1.2.0
assertthat 0.2.1
backports 1.5.0
base64 2.0.1
base64enc 0.1-3
base64url 1.4
basilisk 1.14.3
basilisk.utils 1.14.1
batchelor 1.18.1
bayestestR 0.15.0
beachmat 2.18.1
beanplot 1.3.1
beeswarm 0.4.0
BH 1.87.0-1
BiasedUrn 2.0.12
biglm 0.9-3
bigmemory 4.6.4
bigmemory.sri 0.1.8
Biobase 2.62.0
BiocBaseUtils 1.4.0
BiocFileCache 2.10.1
BiocGenerics 0.48.1
BiocIO 1.12.0
BiocManager 1.30.25
BiocNeighbors 1.20.2
BiocParallel 1.36.0
BiocSingular 1.18.0
BiocStyle 2.30.0
BiocVersion 3.18.1
biocViews 1.70.0
biomaRt 2.58.2
BioQC 1.30.0
Biostrings 2.70.3
biovizBase 1.50.0
bit 4.5.0.1
bit64 4.0.5
bitops 1.0-9
bladderbatch 1.40.0
blob 1.2.4
bluster 1.12.0
bookdown 0.40
brew 1.0-10
brio 1.1.5
broom 1.0.5
broom.helpers 1.15.0
BSgenome 1.70.2
bslib 0.7.0
bsseq 1.38.0
bumphunter 1.44.0
cachem 1.1.0
Cairo 1.6-2
callr 3.7.6
car 3.1-2
carData 3.0-5
caret 6.0-94
caTools 1.18.2
celldex 1.12.0
cellranger 1.1.0
chattr 0.1.0.9002
checkmate 2.3.1
chromVAR 1.24.0
circlize 0.4.16
classInt 0.4-10
cli 3.6.4
clipr 0.8.0
clock 0.7.0
clue 0.3-66
clusterProfiler 4.10.1
clustree 0.5.1
CNEr 1.38.0
coda 0.19-4.1
coin 1.4-3
colorspace 2.1-1
combinat 0.0-8
ComICS 1.0.4
commonmark 1.9.2
ComplexHeatmap 2.18.0
ComplexUpset 1.3.3
CompQuadForm 1.4.3
concaveman 1.1.0
config 0.3.2
conflicted 1.2.0
ConsensusTME 0.0.1.9000
coop 0.6-3
corpcor 1.6.10
corrplot 0.95
covr 3.6.4
cowplot 1.1.3
cpp11 0.5.1
cranlogs 2.1.1
crayon 1.5.3
credentials 2.0.1
crosstalk 1.2.1
cubature 2.1.1
curl 6.2.1
data.table 1.17.0
data.tree 1.1.0
datawizard 0.13.0
DBI 1.2.3
dbplyr 2.4.0
dbscan 1.2.2
DDRTree 0.1.5
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DelayedMatrixStats 1.24.0
deldir 2.0-4
DEoptimR 1.1-3-1
Deriv 4.1.6
desc 1.4.3
DESeq2 1.42.0
devtools 2.4.5
diagram 1.6.5
dichromat 2.0-0.1
diffobj 0.3.5
digest 0.6.37
dir.expiry 1.10.0
DirichletMultinomial 1.44.0
dittoSeq 1.14.3
DMRcate 2.16.1
DMRcatedata 2.20.3
doParallel 1.0.17
doRNG 1.8.6.1
DOSE 3.28.2
dotCall64 1.2
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downloader 0.4
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DT 0.32
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e1071 1.7-16
easyalluvial 0.3.2
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edgeR 4.0.16
ellipse 0.5.0
ellipsis 0.3.2
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entropy 1.3.1
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estimability 1.5.1
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evaluate 1.0.3
exactRankTests 0.8-35
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fastmap 1.2.0
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FDb.InfiniumMethylation.hg19 2.2.0
fgsea 1.28.0
fields 15.2
filelock 1.0.3
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findpython 1.0.9
fitdistrplus 1.1-11
flashClust 1.01-2
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foreach 1.5.2
formatR 1.14
Formula 1.2-5
fs 1.6.5
furrr 0.3.1
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future 1.33.2
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generics 0.1.3
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gert 2.0.1
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gh 1.4.0
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graph 1.80.0
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gridExtra 2.3
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grr 0.9.5
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GSVA 1.48.3
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hardhat 1.3.1
harmony 1.2.0
haven 2.5.4
HDF5Array 1.30.1
hdf5r 1.3.10
HDO.db 0.99.1
HelpersMG 6.1
here 1.0.1
HGNChelper 0.8.1
HiddenMarkov 1.8-14
highr 0.11
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htmlTable 2.4.2
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hwriter 1.3.2.1
ica 1.0-3
ids 1.0.1
ifnb.SeuratData 3.1.0
igraph 2.0.3
IlluminaHumanMethylation450kanno.ilmn12.hg19 0.6.1
IlluminaHumanMethylation450kmanifest 0.4.0
IlluminaHumanMethylationEPICanno.ilm10b2.hg19 0.6.0
IlluminaHumanMethylationEPICanno.ilm10b4.hg19 0.6.0
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NLP 0.2-1
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nortest 1.0-4
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org.Hs.eg.db 3.18.0
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pbv 0.5-47
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plotly 4.10.4
plotrix 3.8-4
plumber 1.3.0
plyr 1.8.9
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polyclip 1.10-6
polynom 1.4-1
poweRlaw 0.80.0
ppcor 1.1
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progress 1.2.3
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RColorBrewer 1.1-3
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scales 1.3.0
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scrime 1.3.5
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scuttle 1.12.0
selectr 0.4-2
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sessioninfo 1.2.2
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SeuratData 0.2.2.9001
SeuratDisk 0.0.0.9021
SeuratObject 5.0.2
SeuratWrappers 0.4.0
sf 1.0-16
SFEData 1.4.0
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shinyWidgets 0.8.2
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Signac 1.12.0
simplifyEnrichment 1.12.0
simstudy 0.8.1
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SingleR 2.4.1
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sitmo 2.0.2
sjlabelled 1.2.0
sjmisc 2.8.9
slam 0.1-50
slider 0.3.1
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sn 2.1.1
snow 0.4-4
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sodium 1.4.0
sourcetools 0.1.7-1
sp 2.1-4
spacexr 2.2.1
spam 2.10-0
SparseArray 1.2.4
SparseM 1.81
sparseMatrixStats 1.14.0
SpatialDecon 1.12.3
SpatialExperiment 1.12.0
SpatialFeatureExperiment 1.4.0
SpatialQC 0.0.0.9000
spatstat.data 3.0-4
spatstat.explore 3.2-7
spatstat.geom 3.2-9
spatstat.random 3.2-3
spatstat.sparse 3.0-3
spatstat.univar 3.0-1
spatstat.utils 3.1-0
spData 2.3.0
spdep 1.3-3
speckle 1.2.0
speedglm 0.3-5
spelling 2.3.0
splancs 2.01-45
SQUAREM 2021.1
standR 1.6.0
statmod 1.5.0
strex 2.0.0
stringdist 0.9.12
stringfish 0.16.0
stringi 1.8.4
stringr 1.5.1
stxBrain.SeuratData 0.1.1
SummarizedExperiment 1.32.0
sva 3.50.0
svglite 2.1.3
swagger 5.17.14.1
sys 3.4.2
systemfonts 1.0.5
TCGAbiolinks 2.30.0
TCGAbiolinksGUI.data 1.22.0
tensor 1.5
tensorA 0.36.2.1
terra 1.8-21
testit 0.13
testthat 3.2.1
textshaping 0.3.7
TFBSTools 1.40.0
TFisher 0.2.0
TFMPvalue 0.0.9
TH.data 1.1-2
tibble 3.2.1
tidygraph 1.3.1
tidyr 1.3.1
tidyselect 1.2.1
tidytree 0.4.6
tidyverse 2.0.0
tiff 0.1-12
timechange 0.3.0
timeDate 4032.109
tinytex 0.51
tm 0.7-12
TrajectoryUtils 1.10.1
treeio 1.26.0
treemap 2.4-4
triebeard 0.4.1
tweenr 2.0.3
TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2
tzdb 0.4.0
UCell 2.6.2
umap 0.2.10.0
units 0.8-5
UpSetR 1.4.0
urlchecker 1.0.1
urltools 1.7.3
usethis 2.2.3
utf8 1.2.4
uuid 1.2-0
uwot 0.2.2
V8 6.0.1
varhandle 2.0.6
VariantAnnotation 1.48.1
vctrs 0.6.5
VGAM 1.1-11
vipor 0.4.7
viridis 0.6.5
viridisLite 0.4.2
visNetwork 2.1.2
vitessceAnalysisR 0.99.0
vitessceR 0.99.0
Voyager 1.4.0
vroom 1.6.5
waldo 0.5.2
warp 0.2.1
webutils 1.2.2
whisker 0.4.1
withr 3.0.0
wk 0.9.1
writexl 1.5.0
xCell 1.1.0
xfun 0.44
XML 3.99-0.17
xml2 1.3.6
xopen 1.0.0
xtable 1.8-4
XVector 0.42.0
yaImpute 1.0-34
yaml 2.3.8
yulab.utils 0.1.4
zellkonverter 1.12.1
zip 2.3.1
zlibbioc 1.48.0
zoo 1.8-12
base 4.3.1
boot 1.3-28
class 7.3-22
cluster 2.1.4
codetools 0.2-19
compiler 4.3.1
datasets 4.3.1
foreign 0.8-82
graphics 4.3.1
grDevices 4.3.1
grid 4.3.1
KernSmooth 2.23-22
lattice 0.21-8
MASS 7.3-60
Matrix 1.6-0
methods 4.3.1
mgcv 1.9-0
nlme 3.1-162
nnet 7.3-19
parallel 4.3.1
rpart 4.1.19
spatial 7.3-15
splines 4.3.1
stats 4.3.1
stats4 4.3.1
survival 3.5-5
tcltk 4.3.1
tools 4.3.1
utils 4.3.1
python 3.9 (conda env)
Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
aiobotocore 2.5.4 pypi_0 pypi
aiofiles 24.1.0 pypi_0 pypi
aiohappyeyeballs 2.4.6 pypi_0 pypi
aiohttp 3.11.13 pypi_0 pypi
aioitertools 0.12.0 pypi_0 pypi
aiosignal 1.3.2 pypi_0 pypi
anndata 0.10.9 pypi_0 pypi
anyio 4.8.0 pypi_0 pypi
anywidget 0.9.15 pypi_0 pypi
argon2-cffi 23.1.0 pypi_0 pypi
argon2-cffi-bindings 21.2.0 pypi_0 pypi
array-api-compat 1.11 pypi_0 pypi
arrow 1.3.0 pypi_0 pypi
asciitree 0.3.3 pypi_0 pypi
asttokens 3.0.0 pyhd8ed1ab_1 conda-forge
async-lru 2.0.4 pypi_0 pypi
async-timeout 5.0.1 pypi_0 pypi
attrs 25.1.0 pypi_0 pypi
babel 2.17.0 pypi_0 pypi
beautifulsoup4 4.13.3 pypi_0 pypi
black 25.1.0 pypi_0 pypi
bleach 6.2.0 pypi_0 pypi
botocore 1.31.17 pypi_0 pypi
bzip2 1.0.8 h4bc722e_7 conda-forge
ca-certificates 2025.2.25 h06a4308_0
certifi 2025.1.31 pypi_0 pypi
cffi 1.17.1 pypi_0 pypi
charset-normalizer 3.4.1 pypi_0 pypi
click 8.1.8 pypi_0 pypi
cloudpickle 3.1.1 pypi_0 pypi
colorcet 3.1.0 pypi_0 pypi
comm 0.2.2 pyhd8ed1ab_1 conda-forge
contourpy 1.3.0 pypi_0 pypi
cycler 0.12.1 pypi_0 pypi
dask 2024.8.0 pypi_0 pypi
dask-expr 1.1.10 pypi_0 pypi
dask-image 2024.5.3 pypi_0 pypi
datashader 0.17.0 pypi_0 pypi
debugpy 1.8.12 py39hf88036b_0 conda-forge
decorator 5.2.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pypi_0 pypi
distributed 2024.8.0 pypi_0 pypi
esbuild-py 0.1.5 pypi_0 pypi
exceptiongroup 1.2.2 pyhd8ed1ab_1 conda-forge
executing 2.2.0 pypi_0 pypi
fasteners 0.19 pypi_0 pypi
fastjsonschema 2.21.1 pypi_0 pypi
fonttools 4.56.0 pypi_0 pypi
fqdn 1.5.1 pypi_0 pypi
frozenlist 1.5.0 pypi_0 pypi
fsspec 2023.6.0 pypi_0 pypi
generate-tiff-offsets 0.1.7 pypi_0 pypi
geopandas 1.0.1 pypi_0 pypi
get-annotations 0.1.2 pypi_0 pypi
h11 0.14.0 pypi_0 pypi
h5py 3.13.0 pypi_0 pypi
httpcore 1.0.7 pypi_0 pypi
httpx 0.28.1 pypi_0 pypi
idna 3.10 pypi_0 pypi
imageio 2.37.0 pypi_0 pypi
importlib-metadata 8.6.1 pyha770c72_0 conda-forge
importlib-resources 6.5.2 pypi_0 pypi
ipykernel 6.29.5 pyh3099207_0 conda-forge
ipython 8.18.1 pyh707e725_3 conda-forge
ipywidgets 8.1.5 pypi_0 pypi
isoduration 20.11.0 pypi_0 pypi
jedi 0.19.2 pyhd8ed1ab_1 conda-forge
jinja2 3.1.5 pypi_0 pypi
jmespath 1.0.1 pypi_0 pypi
joblib 1.4.2 pypi_0 pypi
json5 0.10.0 pypi_0 pypi
jsonpointer 3.0.0 pypi_0 pypi
jsonschema 4.23.0 pypi_0 pypi
jsonschema-specifications 2024.10.1 pypi_0 pypi
jupyter-events 0.12.0 pypi_0 pypi
jupyter-lsp 2.2.5 pypi_0 pypi
jupyter-server 2.15.0 pypi_0 pypi
jupyter-server-proxy 4.4.0 pypi_0 pypi
jupyter-server-terminals 0.5.3 pypi_0 pypi
jupyter_client 8.6.3 pyhd8ed1ab_1 conda-forge
jupyter_core 5.7.2 pyh31011fe_1 conda-forge
jupyterlab 4.3.5 pypi_0 pypi
jupyterlab-pygments 0.3.0 pypi_0 pypi
jupyterlab-server 2.27.3 pypi_0 pypi
jupyterlab-widgets 3.0.13 pypi_0 pypi
kerchunk 0.2.7 pypi_0 pypi
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.7 pypi_0 pypi
krb5 1.21.3 h659f571_0 conda-forge
lazy-loader 0.4 pypi_0 pypi
ld_impl_linux-64 2.43 h712a8e2_4 conda-forge
legacy-api-wrap 1.4.1 pypi_0 pypi
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libffi 3.4.6 h2dba641_0 conda-forge
libgcc 14.2.0 h767d61c_2 conda-forge
libgcc-ng 14.2.0 h69a702a_2 conda-forge
libgomp 14.2.0 h767d61c_2 conda-forge
liblzma 5.6.4 hb9d3cd8_0 conda-forge
liblzma-devel 5.6.4 hb9d3cd8_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libsodium 1.0.20 h4ab18f5_0 conda-forge
libsqlite 3.49.1 hee588c1_1 conda-forge
libstdcxx 14.2.0 h8f9b012_2 conda-forge
libstdcxx-ng 14.2.0 h4852527_2 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
llvmlite 0.43.0 pypi_0 pypi
locket 1.0.0 pypi_0 pypi
markdown-it-py 3.0.0 pypi_0 pypi
markupsafe 3.0.2 pypi_0 pypi
matplotlib 3.9.4 pypi_0 pypi
matplotlib-inline 0.1.7 pyhd8ed1ab_1 conda-forge
mdurl 0.1.2 pypi_0 pypi
mistune 3.1.2 pypi_0 pypi
msgpack 1.1.0 pypi_0 pypi
multidict 6.1.0 pypi_0 pypi
multipledispatch 1.0.0 pypi_0 pypi
multiscale-spatial-image 1.0.1 pypi_0 pypi
mypy-extensions 1.0.0 pypi_0 pypi
natsort 8.4.0 pypi_0 pypi
nbclient 0.10.2 pypi_0 pypi
nbconvert 7.16.6 pypi_0 pypi
nbformat 5.10.4 pypi_0 pypi
ncurses 6.5 h2d0b736_3 conda-forge
negspy 0.2.24 pypi_0 pypi
nest-asyncio 1.6.0 pyhd8ed1ab_1 conda-forge
networkx 3.2.1 pypi_0 pypi
notebook-shim 0.2.4 pypi_0 pypi
numba 0.60.0 pypi_0 pypi
numcodecs 0.12.1 pypi_0 pypi
numpy 1.24.4 pypi_0 pypi
ome-zarr 0.10.2 pypi_0 pypi
openssl 3.4.1 h7b32b05_0 conda-forge
overrides 7.7.0 pypi_0 pypi
packaging 24.2 pyhd8ed1ab_2 conda-forge
pandas 2.2.3 pypi_0 pypi
pandocfilters 1.5.1 pypi_0 pypi
param 2.2.0 pypi_0 pypi
parso 0.8.4 pyhd8ed1ab_1 conda-forge
partd 1.4.2 pypi_0 pypi
pathspec 0.12.1 pypi_0 pypi
patsy 1.0.1 pypi_0 pypi
pexpect 4.9.0 pyhd8ed1ab_1 conda-forge
pickleshare 0.7.5 pyhd8ed1ab_1004 conda-forge
pillow 11.1.0 pypi_0 pypi
pims 0.7 pypi_0 pypi
pip 25.0.1 pyh8b19718_0 conda-forge
platformdirs 4.3.6 pyhd8ed1ab_1 conda-forge
pooch 1.8.2 pypi_0 pypi
prometheus-client 0.21.1 pypi_0 pypi
prompt-toolkit 3.0.50 pyha770c72_0 conda-forge
propcache 0.3.0 pypi_0 pypi
psutil 7.0.0 py39h8cd3c5a_0 conda-forge
psygnal 0.12.0 pypi_0 pypi
ptyprocess 0.7.0 pyhd8ed1ab_1 conda-forge
pure_eval 0.2.3 pyhd8ed1ab_1 conda-forge
pyarrow 19.0.1 pypi_0 pypi
pycparser 2.22 pypi_0 pypi
pyct 0.5.0 pypi_0 pypi
pygments 2.19.1 pyhd8ed1ab_0 conda-forge
pynndescent 0.5.13 pypi_0 pypi
pyogrio 0.10.0 pypi_0 pypi
pyparsing 3.2.1 pypi_0 pypi
pyproj 3.6.1 pypi_0 pypi
python 3.9.21 h9c0c6dc_1_cpython conda-forge
python-dateutil 2.9.0.post0 pyhff2d567_1 conda-forge
python-json-logger 3.2.1 pypi_0 pypi
python_abi 3.9 5_cp39 conda-forge
pytz 2025.1 pypi_0 pypi
pywavelets 1.6.0 pypi_0 pypi
pyyaml 6.0.2 pypi_0 pypi
pyzmq 26.2.1 py39h4e4fb57_0 conda-forge
readline 8.2 h8c095d6_2 conda-forge
referencing 0.36.2 pypi_0 pypi
requests 2.32.3 pypi_0 pypi
rfc3339-validator 0.1.4 pypi_0 pypi
rfc3986-validator 0.1.1 pypi_0 pypi
rich 13.9.4 pypi_0 pypi
rpds-py 0.23.1 pypi_0 pypi
s3fs 2023.6.0 pypi_0 pypi
scanpy 1.10.3 pypi_0 pypi
scikit-image 0.20.0 pypi_0 pypi
scikit-learn 1.6.1 pypi_0 pypi
scipy 1.9.1 pypi_0 pypi
seaborn 0.13.2 pypi_0 pypi
send2trash 1.8.3 pypi_0 pypi
session-info 1.0.0 pypi_0 pypi
setuptools 75.8.2 pyhff2d567_0 conda-forge
shapely 2.0.7 pypi_0 pypi
simpervisor 1.0.0 pypi_0 pypi
six 1.17.0 pyhd8ed1ab_0 conda-forge
slicerator 1.1.0 pypi_0 pypi
sniffio 1.3.1 pypi_0 pypi
sortedcontainers 2.4.0 pypi_0 pypi
soupsieve 2.6 pypi_0 pypi
spatial-image 1.1.0 pypi_0 pypi
spatialdata 0.2.5.post0 pypi_0 pypi
sqlite 3.49.1 h9eae976_1 conda-forge
stack_data 0.6.3 pyhd8ed1ab_1 conda-forge
starlette 0.14.0 pypi_0 pypi
statsmodels 0.14.4 pypi_0 pypi
stdlib-list 0.11.1 pypi_0 pypi
tblib 3.0.0 pypi_0 pypi
terminado 0.18.1 pypi_0 pypi
threadpoolctl 3.5.0 pypi_0 pypi
tifffile 2020.10.1 pypi_0 pypi
tinycss2 1.4.0 pypi_0 pypi
tk 8.6.13 noxft_h4845f30_101 conda-forge
tomli 2.2.1 pypi_0 pypi
toolz 1.0.0 pypi_0 pypi
tornado 6.4.2 py39h8cd3c5a_0 conda-forge
tqdm 4.67.1 pypi_0 pypi
traitlets 5.14.3 pyhd8ed1ab_1 conda-forge
types-python-dateutil 2.9.0.20241206 pypi_0 pypi
typing_extensions 4.12.2 pyha770c72_1 conda-forge
tzdata 2025.1 pypi_0 pypi
ujson 5.10.0 pypi_0 pypi
umap-learn 0.5.7 pypi_0 pypi
uri-template 1.3.0 pypi_0 pypi
urllib3 1.26.20 pypi_0 pypi
uvicorn 0.34.0 pypi_0 pypi
vitessce 3.4.2 pypi_0 pypi
wcwidth 0.2.13 pyhd8ed1ab_1 conda-forge
webcolors 24.11.1 pypi_0 pypi
webencodings 0.5.1 pypi_0 pypi
websocket-client 1.8.0 pypi_0 pypi
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
widgetsnbextension 4.0.13 pypi_0 pypi
wrapt 1.17.2 pypi_0 pypi
xarray 2024.7.0 pypi_0 pypi
xarray-dataclasses 1.9.1 pypi_0 pypi
xarray-datatree 0.0.15 pypi_0 pypi
xarray-schema 0.0.3 pypi_0 pypi
xarray-spatial 0.4.0 pypi_0 pypi
xz 5.6.4 hbcc6ac9_0 conda-forge
xz-gpl-tools 5.6.4 hbcc6ac9_0 conda-forge
xz-tools 5.6.4 hb9d3cd8_0 conda-forge
yarl 1.18.3 pypi_0 pypi
zarr 2.18.2 pypi_0 pypi
zeromq 4.3.5 h3b0a872_7 conda-forge
zict 3.0.0 pypi_0 pypi
zipp 3.21.0 pyhd8ed1ab_1 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge