sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
fd5d9141b50eb68d30b5c34727a145ff0ef6c143557cabf18f56fcd16d6d6c6e | Shell | 207 | 9 | #!/bin/bash
set -e
samtools view -h resources/bc_anchored_10_reads.sorted.bam \
| sed s/C+m?,/C+Z,/g \
| sed s/C+h?,/C+Y,/g \
| samtools view -b -o resources/bc_anchored_10_reads_old_tags.bam
|
cb6bc252dd4e6d2040d41236afb93c95032d3816ab9af9785c4acb6da5b27ff0 | Shell | 237 | 4 | CUDA_VISIBLE_DEVICES=7 python evaluate_mmd.py --dt 0.01 --kappa 0.8 \
--seeds 0 1 12 123 1234 \
--models OnsagerRegL21e-3 OnsagerRegL21e-4 OnsagerRegSobolev1e-3 OnsagerRegSobolev1e-4 \
--out-name mmd_summary_OnsagerReg_dt0.01 |
1470af376d2cafb148ecf67ba8cc598ea90805142a72850c0598dbd575346cab | Shell | 325 | 12 | #!/bin/bash
#SBATCH --job-name=i23pinml
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=24
#SBATCH --gres=gpu:4
#SBATCH --partition=cs05r
#SBATCH --time=23:59:59
#SBATCH --output=./fromslurm.log
tfimage=/path/to/tensorflow_2.8.2-gpu-jupyter.sif
singularity exec --nv --home $PWD $tfimage python /path/to/img_classificati... |
a07fecd22305cee04b11d4a533b0aa327c3f9cfa892338fbd184f3b5e2c23292 | Shell | 373 | 10 | #!/usr/bin/env bash
set -e
pushd resources
samtools view -C -T CGI_ladder_3.6kb_ref.fa bc_anchored_10_reads.sorted.bam > bc_anchored_10_reads.sorted.cram
samtools index bc_anchored_10_reads.sorted.cram
samtools view -C -T CGI_ladder_3.6kb_ref.fa bc_anchored_10_reads.unmapped.bam > bc_anchored_10_reads_unmapped.cram
s... |
d0eac509d92986b24d6d824e4c599e5c3309b26922322eb01073efe7bff10c9b | Shell | 424 | 9 | # !/bin/bash
nohup bash -c "CUDA_VISIBLE_DEVICES=0 python main_sgld.py model.seed=10" > s10.file 2>&1 &
nohup bash -c "CUDA_VISIBLE_DEVICES=1 python main_sgld.py model.seed=20" > s20.file 2>&1 &
nohup bash -c "CUDA_VISIBLE_DEVICES=2 python main_sgld.py model.seed=30" > s30.file 2>&1 &
nohup bash -c "CUDA_VISIBLE_DEVIC... |
0cbc5708b17cc659d4e2ab1ab99224b379f539326744d234286f0c479bd000ab | Shell | 494 | 12 | for file in src/aind_data_schema_models/_generators/templates/*.txt; do
# Extract the filename without the directory and extension
type_name=$(basename "$file" .txt)
# If harp_type, run the update script
if [ "$type_name" == "harp_types" ]; then
python src/aind_data_schema_models/_generators/up... |
017e4372366d12323ba5a770144e4fd9534eb5c978066128d3250b4dd3c35dd1 | Shell | 521 | 21 | #!/bin/bash
# this script makes some reads that have their ends trimmed
set -eu
python ./trim_reads.py \
resources/bc_anchored_10_reads.sorted.bam \
./trimmed.bam \
--head-trim 25 \
--tail-trim 30
samtools fastq trimmed.bam > trimmed.fastq
minimap2 -ax map-ont \
./resources/CGI_ladder_3.6kb_ref.fa \
t... |
e2045a36ccd06bddfc10a8c6123211e30e3302db89e75d39cd61713f1984e128 | Shell | 528 | 9 | #!/bin/bash
nohup bash -c "CUDA_VISIBLE_DEVICES=2 python main_reduced_polymerF.py Model_name=HD2 model.seed=0" > l0.file 2>&1 &
nohup bash -c "CUDA_VISIBLE_DEVICES=3 python main_reduced_polymerF.py Model_name=HD2 model.seed=1" > l1.file 2>&1 &
nohup bash -c "CUDA_VISIBLE_DEVICES=2 python main_reduced_polymerF.py Mode... |
e6d98044bf89acfa40ab059045cda31c6cd3850a1761df5f85dfb22cd0d2de3c | Shell | 530 | 27 | # Shared bash functions used in testing
# Print a title to separate tests in logs.
title() {
# Record and disable xtrace to reduce noise
local had_xtrace=0
case $- in
*x*) had_xtrace=1;
set +x ;;
esac
# Create a line of `=` 80 characters wide
local n_cols=80
local line=$(p... |
96e40591a9f11e85ee0593a78dd71b2727e56796aa6b43b46f8bd7e336ad38be | Shell | 628 | 27 | # to install sigpy from scratch:
git clone https://github.com/ZhengguoTan/sigpy.git sigpy_github
cd sigpy_github
conda create -n sigpy_github python=3.11
conda activate sigpy_github
conda install -c anaconda pip
python -m pip install torch torchvision torchaudio
python -m pip install tqdm
python -m pip install nu... |
b1057dcd7bc2ae64efb53c3f6aefb01cc4580f06aeda55507dbc54e557a34e36 | Shell | 660 | 22 | #! /bin/bash
set -vex
CWD=$(pwd)
out_dir=temp
mkdir -p ${out_dir}
pushd ${out_dir}
region="chr20"
threads="4"
in_ref="${CWD}/../test-02-supertiny/in.ref.fasta.gz"
in_bam="${CWD}/../test-02-supertiny/in.aln.bam"
${KADAYASHI_BIN} --version 2>&1 | tee kadayashi.version.txt
${KADAYASHI_BIN} varcall -r ${region} -o varcal... |
04b43fcef21ecc5fa3e44f72b9802a6c9e55fd279cfc1d559747d1d5b303f63e | Shell | 670 | 22 | #!/usr/bin/env bash
set -euo pipefail
source config/project_config.sh
mkdir -p logs
echo "========== BAM output check =========="
expected=$(awk -F',' 'NR>1 {print $2}' "$SAMPLE_INFO" | wc -l)
found=$(find bam -maxdepth 1 -name '*_sorted.bam' | wc -l)
echo "Expected sorted BAM: ${expected}"
echo "Found sorted BAM: ... |
4d9462e28eba1ae2fa1e95e57b44ec99c18054c8cb643d0780ea6b2cbe753a15 | Shell | 672 | 18 | #!/usr/bin/env bash
# Project-level configuration. Edit here only if your server policy requires it.
set -euo pipefail
# Use no more than 8 threads for a single task on shared servers.
THREADS=${THREADS:-8}
# Disk safety threshold in GB. Pipeline stops if available disk is below this value.
MIN_FREE_GB=${MIN_FREE_GB:... |
50c60f0b0e827f611e4780adfe3a803a942f59cca4e710dbe7e333ca348455ec | Shell | 687 | 39 | #!/bin/bash
if [ -z $1 ]; then
echo "USAGE: $0 old_tsv"
exit 1
fi
set -eu
function realpath () {
python -c "import os; print(os.path.realpath('${1}'))"
}
old=$(realpath $1)
pushd ../
cargo b --release
popd
modkit=$(realpath ../target/release/modkit)
${modkit} \
extract \
/Users/art.rand/projects/mod... |
ae1481790e3fdf5e2542a021decb88a467f2a8c106695ca5657ae4f61e9e7416 | Shell | 705 | 23 | #!/usr/bin/env bash
set -euo pipefail
source config/project_config.sh
mkdir -p reference/hisat2_index logs
if [[ ! -s "$GENOME_FA" ]]; then
echo "Downloading ${GENOME_NAME} reference genome..."
tmp_gz="${GENOME_FA}.gz"
wget -c "$GENOME_FA_URL" -O "$tmp_gz"
gzip -dc "$tmp_gz" > "$GENOME_FA"
else
echo "Refere... |
a714c7bdc18968970bd5fa1de5887771576d622331a56e2fb3da36bf047f15a2 | Shell | 805 | 14 | # !/bin/bash
nohup bash -c "CUDA_VISIBLE_DEVICES=0 python main_Kaczmarz_scale.py data.batch_size=1" > l1.file 2>&1 &
nohup bash -c "CUDA_VISIBLE_DEVICES=1 python main_Kaczmarz_scale.py data.batch_size=4" > l4.file 2>&1 &
nohup bash -c "CUDA_VISIBLE_DEVICES=2 python main_Kaczmarz_scale.py data.batch_size=16" > l16.file... |
410b2d430f16ca4d494f7dc9e991f8a8d020826df44da312bc1ef78f2e961e22 | Shell | 842 | 28 | #!/usr/bin/env bash
set -euo pipefail
echo "========== Software environment check =========="
softwares=("prefetch" "fasterq-dump" "fastp" "hisat2" "hisat2-build" "samtools" "Rscript" "gzip" "awk" "df")
missing=0
for soft in "${softwares[@]}"; do
if command -v "$soft" >/dev/null 2>&1; then
printf "[OK] %-15s %s\... |
e0c4170d31e029b2dd558a19dfb023d52f8a17e029f0ddbde3cdfe20e2aae04d | Shell | 849 | 34 | #!/bin/bash
#
# Wrapper around bash to keep the cram test output around so we can check it if
# it fails in CI.
#
# cram calls the shell with "$0 -" then pipes the args in via stdin, so we only
# need to emulate that much.
#
if [[ $# -ne 1 ]] ; then
echo "Unexpected args"
exit 1
elif [[ -z ${TESTFILE} ]] ; then... |
a355084fd8d3febdc43a17531de43e9240e51ad102bd118ef865eca1c2fc961c | Shell | 900 | 23 | #!/bin/bash
DOCKER_SOCKET=/var/run/docker.sock
# In order run DooD (Docker outside of Docker) we need to make sure the
# container's docker group id matches the host's group id. If it doens't match,
# update the group id and then restart the script. (also remove sudoer privs)
if [ ! -S ${DOCKER_SOCKET} ]; then
ech... |
ca26a1904c08dab9db60df4317be11e401989559df28b4e722780eef8ee5ee2a | Shell | 919 | 32 | #!/bin/bash
# how to write it out: ./running_biasfield_job_t1_reg.sh -n $SUBJECT
#gets displayed when -h or --help is put in
display_usage(){
echo "***************************************************************************************
Script for biasfield correction
**********************************************... |
942bc1f5fad1b5d464900d92c6267f611039cc20de7936045948987d1a7faac2 | Shell | 960 | 40 | #!/bin/sh
set -u
SCRIPT_DIR="$(CDPATH= cd -- "$(dirname -- "$0")" && pwd)"
cd "$SCRIPT_DIR"
GPU_ID="${GPU_ID:-1}"
KAPPA="${KAPPA:-0.8}"
DTS="${DTS:-0.01 0.005}"
SEEDS="${SEEDS:-0 1 12 123 1234}"
mkdir -p running_log
log_file="running_log/evaluate_mmd.file"
failed=0
for dt in $DTS; do
echo "===== evaluate_mmd dt=... |
b38402f379d5d39756a601ed655654111c0d8d969ce5b0cb162b5d84aa613445 | Shell | 979 | 30 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --mem=4GB
#SBATCH --partition={your-partition}
#SBATCH --time=2:00:00
# modify this section to make the nextflow command available to your environment
# e.g., using a conda environment with nextflow installed
conda activate env_nf
PIPELINE_PATH="path-t... |
584e7d65b291b8b49e7d6ed173c01b4ff638b7f0952177546b6dfebf68d64601 | Shell | 985 | 30 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --mem=4GB
#SBATCH --partition={your-partition}
#SBATCH --time=2:00:00
# modify this section to make the nextflow command available to your environment
# e.g., using a conda environment with nextflow installed
conda activate env_nf
PIPELINE_PATH="path-t... |
80365a254b4a4b5bae95c76a911e93acbb3f762f1389eff68e33d0e0fe8e3361 | Shell | 988 | 32 | #!/bin/bash
# how to write it out: ./running_biasfield_job_t1_reg.sh -n $SUBJECT
#gets displayed when -h or --help is put in
display_usage(){
echo "***************************************************************************************
Script for biasfield correction
**********************************************... |
b4bc76f90cf9f535ef27108597a66a4cb23319539519138e7e3db982b4fccbaa | Shell | 998 | 35 | #!/bin/bash
set -ex
if [[ $# -lt 2 ]]; then
echo "Usage: $0 <dorado executable> <pod5_dir> [device_string]"
echo " <pod5_dir> should contain large input files"
exit 1
fi
pod5_dir=${2}
device_string=${3:-"auto"}
echo "Using device string -x $device_string"
dorado_bin=$(cd "$(dirname $1)"; pwd -P)/$(basen... |
fea34cc45337f669259d9a56bdf817174e8ac69cf93475a48d4e958d68d6fc5a | Shell | 1,041 | 21 | IMAGES_ARG="${1:-base,nwb,ks25,ks4}"
IFS=',' read -r -a IMAGES_LIST <<< "$IMAGES_ARG"
SPIKEINTERFACE_VERSION=$(grep '^spikeinterface==' requirements.txt | cut -d'=' -f3)
if [[ " ${IMAGES_LIST[*]} " == *" base "* ]]; then
echo "Building base image..."
docker build -t ghcr.io/allenneuraldynamics/aind-ephys-pipe... |
802bfd1d1c132bbbccfd1f5fcbb78ceae887a5a03c4ae42de6a70efcdc89a01b | Shell | 1,112 | 39 | #!/bin/bash
# how to write it out: ./running_transformix.sh -f fixed_image -o output_dir -t params -n outputname
#gets displayed when -h or --help is put in
display_usage(){
echo "***************************************************************************************
Script for transformix in bash
***************... |
f3ae4ec8d77f5d364b26bbd6cb5b50d97c37d41f9491425b1b5520d865b384bf | Shell | 1,203 | 27 | #!bin/bash
REGION_BED="/home3/ciervo/scMULTIOME/Analisi/scRNA_scATAC/malignant_consensusPeaks.bed"
GENOME_FASTA="/storage/qnap_vol1/SHARED/NGSTOOLS/BCBIO2023/genomes/Hsapiens/hg38/seq/hg38.fa"
CHROMSIZES="/home3/ciervo/scMULTIOME/Analisi/scRNA_scATAC/hg38.chrom.sizes"
SCRIPT_DIR="/home3/ciervo/scMULTIOME/Analisi/scRNA_... |
3145d003fad65b76f2772b2131e0725c472d3dcd4a562b5d26591875227a55bc | Shell | 1,218 | 37 | #!/bin/bash
#will copy biascorrected to a new folder
#how to write it out: ./eeg_removal.sh -n racsleep08 -d /autofs/cluster/ldl/nina/pet_eeg_fmri
#gets displayed when -h or --help is put in
display_usage(){
echo "***************************************************************************************
script to ... |
a896ef0d787075072cd13e2c1729f52a4e040965c591cc8729103d88522a1930 | Shell | 1,218 | 39 | #!/bin/bash
# how to write it out: ./running_elastix.sh -f fixed_image -m moving_image -o output_dir -p param_file -n outputfilename
#gets displayed when -h or --help is put in
display_usage(){
echo "***************************************************************************************
Script for elastix in... |
d5b972d674169bfcd11be143ac6f6b666bcf8735846e4c8c793b2f39e6403441 | Shell | 1,240 | 25 | #!/bin/bash
#SBATCH --job-name=biasfieldjuly8th
#SBATCH --output=%x_%j.out
#SBATCH --mail-user="n.e.fultz@lumc.nl"
#SBATCH --mail-type="ALL"
#SBATCH --partition="gpu"
#SBATCH --time=48:00:00
#SBATCH --mem=40GB
#SBATCH --gres=gpu:1
## How to set the above SBATCH setting
# job-name: indicate the name for this job (doesn... |
b8b2eea3c94f11420aa733144d1715de1f84e0cfe06b406293594ccbb5f16a2c | Shell | 1,334 | 36 | # this needs to run in an env with spikeinterface/pynwb/neuroconv installed
NXF_VER=25.04.1
# get all input arguments into a variable
INPUT_ARGS="$@"
echo "Input arguments: $INPUT_ARGS"
SCRIPT_PATH="$(realpath "$0")"
echo "Running script at: $SCRIPT_PATH"
SAMPLE_DATASET_PATH="$(realpath $(dirname "$SCRIPT_PATH")/..... |
a32c82b8775a2ea6c0152dc61cf4baf871629269dfb91039ec1ba04360589ef0 | Shell | 1,337 | 56 | #!/bin/bash
usage() {
cat << EOF
Usage: direct SUBJECT_ID OUTPUT_DIR
Continue DL+DiReCT starting from an existing segmentation in OUTPUT_DIR
EOF
exit 0
}
die() {
echo "ERROR: $1"
exit 1
}
# defaults
if [ -z "${ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS}" ] ; then
# number of threads for DiReCT
export ITK_GLOBAL_DEF... |
2f0820a5808c2957644f0a7b51edc68a25909212c000de6d5d311abba12c5177 | Shell | 1,338 | 36 | # this needs to run in an env with spikeinterface/pynwb/neuroconv installed
NXF_VER=25.04.1
# get all input arguments into a variable
INPUT_ARGS="$@"
echo "Input arguments: $INPUT_ARGS"
SCRIPT_PATH="$(realpath "$0")"
echo "Running script at: $SCRIPT_PATH"
SAMPLE_DATASET_PATH="$(realpath $(dirname "$SCRIPT_PATH")/..... |
3e17fce951a07326e22039df359cf8238ca1cd68c0b4ea4fc5ed037b9fe15e5c | Shell | 1,374 | 47 | #!/bin/bash
set -eo pipefail
source scripts/add-user-docker.sh
# this doesn't protect from docker but it's a little more secure
export PYTHONPATH=$AIRFLOW_HOME/common:$PYTHONPATH
echo "start script with group $DOCKER_GROUP"
if [[ -z "${_AIRFLOW_DB_UPGRADE=}" ]] ; then
python scripts/install_packages.py
else
... |
0c0d58195dce7a4f1f7d7b2037c7585782d9802566ba4ba7e62ea451d13d10e5 | Shell | 1,390 | 62 | #!/bin/bash
# Integration tests for Dorado Correct.
set -ex
set -o pipefail
if [[ $# -lt 1 ]]; then
echo "Usage: $0 <dorado executable> [<out_dir>]"
exit 1
fi
if [[ $# -eq 2 ]]; then
mkdir -p $2
fi
# CLI options.
IN_DORADO_BIN="$1"
OUT_DIR="$2"
TEST_DIR=$(cd "$(dirname $0)"; pwd -P)
TEST_DATA_DIR=${TE... |
816ff5c4bf14f547189796daad14abc7499529d8bfe8e37bd30c12bc3e010dcc | Shell | 1,420 | 39 | #!/bin/bash
function create_www_user() {
local local_password=""
# Warning: command environment variables (*_CMD) have priority over usual configuration variables
# for configuration parameters that require sensitive information. This is the case for the SQL database
# and the broker backend in this ent... |
443e5e30f484fd9c447958751e1a2097b42e56f262e6fa56a567b5d4e9e1e8a7 | Shell | 1,476 | 26 | #!/bin/bash
#SBATCH --job-name=biasfieldjuly8th
#SBATCH --output=%x_%j.out
#SBATCH --mail-user="n.e.fultz@lumc.nl"
#SBATCH --mail-type="ALL"
#SBATCH --partition="gpu"
#SBATCH --time=48:00:00
#SBATCH --mem=40GB
#SBATCH --gres=gpu:1
## How to set the above SBATCH setting
# job-name: indicate the name for this job (... |
5fb5eefd79603baf57100097ed9d26a2061f893f27329e7705cc4fee907902b6 | Shell | 1,498 | 54 | #!/bin/bash
# Test expected log output from the dorado binary execution.
set -ex
set -o pipefail
test_dir=$(dirname $0)
dorado_bin=$(cd "$(dirname $1)"; pwd -P)/$(basename $1)
model=${2:-dna_r10.4.1_e8.2_400bps_hac@v5.0.0}
batch=${3:-384}
data_dir=${test_dir}/data
output_dir_name=test_logging_output_${RANDOM}
output... |
715bcb1710bc68748cc71c7f1e2d949553211d27631045c8370a235d73d879b2 | Shell | 1,501 | 25 | #!/bin/bash
#SBATCH --job-name=biasfieldjuly8th
#SBATCH --output=%x_%j.out
#SBATCH --mail-user="n.e.fultz@lumc.nl"
#SBATCH --mail-type="ALL"
#SBATCH --partition="gpu"
#SBATCH --time=48:00:00
#SBATCH --mem=40GB
#SBATCH --gres=gpu:1
## How to set the above SBATCH setting
# job-name: indicate the name for this job (doesn... |
1b14ae0f342779fea085b599b0fae0867315a8b6408b275da35318f0046c03e7 | Shell | 1,521 | 49 | #!/bin/bash
is_ctg=0
if [ $# -gt 1 ] && [ $1 == '-A' ]; then
is_ctg=1
shift
fi
if [ $# -lt 2 ]; then
echo "Usage: $0 [-A] <prefix> <gene>"
exit 1
fi
preres="resource-human-HLA"
root=`dirname $0`
pre=$1.$2
touch $pre.gt
if [ ! -s $pre.fq ]; then
echo '** Empty input file. Abort!' >&2
exit 0
fi
if [ $is_ctg -... |
be69a7ed0503dfc7f858cd1e3adde93c9efb7450ecbf601a6a69847bc7f92dd7 | Shell | 1,571 | 26 | #!/bin/bash
#SBATCH --job-name=biasfieldjuly8th
#SBATCH --output=%x_%j.out
#SBATCH --mail-user="n.e.fultz@lumc.nl"
#SBATCH --mail-type="ALL"
#SBATCH --partition="gpu"
#SBATCH --time=48:00:00
#SBATCH --mem=40GB
#SBATCH --gres=gpu:1
## How to set the above SBATCH setting
# job-name: indicate the name for this job (doesn... |
723ba10a4a203603b4dfede10309b370a4681ea8e83c0971b5e489aaf7bed822 | Shell | 1,619 | 29 | #!/bin/bash
#SBATCH --job-name=recons_pvs01
#SBATCH --output=%x_%j.out
#SBATCH --mail-user="n.e.fultz@lumc.nl"
#SBATCH --mail-type="ALL"
#SBATCH --partition="gpu"
#SBATCH --time=48:00:00
#SBATCH --mem=40GB
#SBATCH --gres=gpu:1
## How to set the above SBATCH setting
# job-name: indicate the name for this job (... |
3e1483fe652319b2aeab51be2fa79cb9430b8771f4b3be8678bda487589e416a | Shell | 1,647 | 47 | # test pipeline with sample_nwb file
# DOCKER_IMAGE="ghcr.io/allenneuraldynamics/aind-ephys-pipeline-nwb:si-0.102.1"
NXF_VERSION="25.04.1"
# Check if arguments are passed
if [ "$#" -gt 0 ]; then
ARGS="$@"
echo "Arguments passed: $ARGS"
else
ARGS=""
echo "No arguments passed"
fi
SCRIPT_PATH="$(realpath... |
3e94b9062bf02a682336f5dbeb93b86c5d4e4e189a316a3b23fa3cfdfd1b7fc4 | Shell | 1,704 | 28 | IMAGES_ARG="${1:-base,nwb,ks25,ks4}"
IFS=',' read -r -a IMAGES_LIST <<< "$IMAGES_ARG"
SPIKEINTERFACE_VERSION=$(grep '^spikeinterface==' requirements.txt | cut -d'=' -f3)
if [[ " ${IMAGES_LIST[*]} " == *" base "* ]]; then
echo "Pushing base image with SpikeInterface version $SPIKEINTERFACE_VERSION"
docker tag ... |
908bde08bb19ce3993261c2dbdb60adcc941ad9bcd8558f53136e2ce595b84c3 | Shell | 1,765 | 69 | #!/bin/bash
abort() {
echo >&2 '
***************
*** ABORTED ***
***************
'
echo "Test failure" >&2
exit 1
}
function realpath () {
python -c "import os; print(os.path.realpath('${1}'))"
}
trap 'abort' 0
set -eu
cargo check
# test_extract_correct_output
cargo run extract \
tests/resou... |
528d94acfd9561320b591b2617942335ff825f62e9b6e0ca3fef024e306d7391 | Shell | 1,886 | 25 | #!/bin/bash
nohup bash -c "CUDA_VISIBLE_DEVICES=1 python linear_case.py Model_name=HD2 model.seed=1 data.var=1" > l3.file 2>&1 &
nohup bash -c "CUDA_VISIBLE_DEVICES=2 python linear_case.py Model_name=HD2 model.seed=10 data.var=1" > l1.file 2>&1 &
nohup bash -c "CUDA_VISIBLE_DEVICES=3 python linear_case.py Model_name=H... |
dc14466f6ac145b878a61e8b095340f38724af6200a6f611fd5ef52a7e39dbd0 | Shell | 1,900 | 61 | #!/bin/bash
# how to write it out: ./registration.sh -n inkref_07_cap -d /home/nefultz/highres_pvs
# nina fultz july 2024
#gets displayed when -h or --help is put in
display_usage(){
echo "***************************************************************************************
Script for registration for high res ... |
95383b34c517b511ecc624aea87043aadf1cbae13db14a403a513ed2dcc73c5a | Shell | 1,972 | 67 | #!/bin/bash
# Usage: ./anats2niftis.sh -s subjDir
# Display help/usage when -h or --help is specified
display_usage(){
echo "***************************************************************************************
Script for processing anatomical NIfTI files in bash
***********************************************... |
41f3c48292d9a806b07916b547f98c4e6e153f86c32a1913ee004e7d1a0a8bbd | Shell | 2,008 | 57 | #!/bin/bash
# Define the base project path
BASE_DIR="/exports/gorter-hpc/users/ninafultz/csfdonuts_lydiane"
# List of special cases where the T1 filename is different
SPECIAL_CASES=("20201014_Reconstruction" "20201016_Reconstruction" "20201008_Reconstruction")
# Loop through all subject folders in the base directory... |
b05c0b0db973e66c6807e5f8e55834886faf19c9be1863e7b0df6c20bd107fbe | Shell | 2,030 | 80 | #!/bin/bash
# Integration tests for Dorado Polish.
set -ex
set -o pipefail
if [[ $# -lt 1 ]]; then
echo "Usage: $0 <dorado executable> [<out_dir>]"
exit 1
fi
if [[ $# -eq 2 ]]; then
mkdir -p $2
fi
# CLI options.
IN_DORADO_BIN="$1"
OUT_DIR="$2"
TEST_DIR=$(cd "$(dirname $0)"; pwd -P)
TEST_DATA_DIR=${TES... |
0ee79bf5db7263948f9256417632f47a663c22c415457b21e1a0123c168a0f06 | Shell | 2,036 | 59 | #!/bin/bash
# Define the base project path
BASE_DIR="/exports/gorter-hpc/users/ninafultz/csfdonuts_lydiane"
# List of special cases where the T1 filename is different
SPECIAL_CASES=("20201014_Reconstruction" "20201016_Reconstruction" "20201008_Reconstruction")
# Loop through all subject folders in the base directory... |
8612925a8684405d4b88903ad2fd41b2d5a1bb96ed6cfb5aa635f8e9ba05ef92 | Shell | 2,061 | 49 | function prepare_mock_data {
# Create a micro BAM file of only 1 record in the current directory.
# The model name (in the header) of the original test data BAM will be replaced with
# the target_model value.
local in_bam="$1"; shift
local target_model="$1"; shift # E.g. "dna_r10.4.1_e8.2_400bp... |
5f5f4500e415243363f07c7007bb5937bc8f358a7ccab976459af3f666454647 | Shell | 2,090 | 50 | #!/bin/bash
#SBATCH -n 32
#SBATCH -t 3-00:00
#SBATCH -N 1
#SBATCH -o %x_%j.o
#SBATCH -e %x_%j.e
#SBATCH --mem=128G
hostname
####################################
## to plot strain differences
#<<MERGE
DIR=/Users/bbae/BB_EXP012_CH... |
074ca9741ad17edd33087db014a33c0b8e9bad7da440fa7cec01f0eb54c056e6 | Shell | 2,183 | 92 | #! /bin/bash
set -e
cargo build
rm book/src/advanced_usage.md
cp advanced_usage.template book/src/advanced_usage.md
doc_file=book/src/advanced_usage.md
echo "" >> ${doc_file}
echo "" >> ${doc_file}
echo "\`\`\`text" >> ${doc_file}
./target/debug/modkit --help >> ${doc_file}
echo "\`\`\`" >> ${doc_file}
subcommand... |
d3d87d6d005e477931acba5ae4283737057529750a5ff899d6bf624600202fe1 | Shell | 2,280 | 102 | #!/bin/bash
set -euo pipefail
if [[ $# -ne 1 ]]; then
echo "Usage: $0 <input.bam>"
exit 1
fi
if ! command -v samtools >/dev/null 2>&1; then
echo "Error: samtools is required but was not found in PATH."
exit 1
fi
input_bam=$1
if [[ ! -f "${input_bam}" ]]; then
echo "Error: input BAM does not exi... |
a764e82f0528abce305f0d4fec6a3a120c5a0bbe4a5130096f92b2ef172b6fdc | Shell | 2,294 | 47 | #!/bin/bash
# Script to do subarachnoid removal
# Usage: ./eeg_removal.sh -n <subject_name> -d <directory_path> -f <func_suffix>
display_usage(){
echo "***************************************************************************************
script to do subarachnoid removal
****************************************... |
f741342161669478aa7828d118249352b680ed672dc16c7f3f611f1aef47d246 | Shell | 2,319 | 86 | #!/bin/bash
# Integration tests for Dorado Polish.
set -ex
set -o pipefail
if [[ $# -lt 1 ]]; then
echo "Usage: $0 <dorado executable> [<out_dir>]"
exit 1
fi
if [[ $# -eq 2 ]]; then
mkdir -p $2
fi
# CLI options.
IN_DORADO_BIN="$1"
OUT_DIR="$2"
TEST_DIR=$(cd "$(dirname $0)"; pwd -P)
TEST_DATA_DIR=${TES... |
423239b102d835f1e6e07efc7fd49b43d9051e2244003e05e796de8c2e306037 | Shell | 2,328 | 71 | #!/bin/bash
# Script log to get data from scanner
# Nina Fultz January 2022
# how to write it out: ./get_data.sh -n dicoms -d /users/ninafultz/cluster_headache/{} -s dcm2niix
#gets displayed when -h or --help is put in
display_usage(){
echo "************************************************************************... |
6924bc7b28f43216fc26fcef6c69fefc31078f1ae8921a567c7d7a41bee8d2c6 | Shell | 2,332 | 71 | # Test pipeline with sample_nwb file on slurm
# Steps to run the test script on SLURM:
# * Appropriate resources allocation, e.g.
# `salloc -N 1 -n 12 -t 00:30:00 --gres=gpu:1 --mem=32G`
# * Environment with nextflow and the required dependencies installed
# e.g., create an environment.yml file with the follo... |
a9d32f8cd2c49a66d7e0e96e7b7c819fc6c3c7d45f7957ac416f8aecdbf9166e | Shell | 2,357 | 66 | #!/bin/bash
# Usage information
display_usage() {
echo "***************************************************************************************"
echo "Script to take bias corrected, eroded, skull mask and apply it to MEMPRAGE to remove EEG artifact."
echo "**************************************************... |
b2b8925245b534a9eacbb8029495f7113e68bd208440f3614abb80f659f17cb1 | Shell | 2,392 | 65 | # test pipeline with sample_nwb file
# DOCKER_IMAGE="ghcr.io/allenneuraldynamics/aind-ephys-pipeline-nwb:si-0.102.1"
# NXF_VERSION="25.04.1"
NXF_VERSION="26.04.0"
# Check if arguments are passed
if [ "$#" -gt 0 ]; then
ARGS="$@"
echo "Arguments passed: $ARGS"
else
ARGS=""
echo "No arguments passed"
fi... |
c1edb8066ac7b2edfdbf1faf9d1d219a853d2cfaa63f4c6e65b674ea37d7c7a5 | Shell | 2,523 | 91 | #!/bin/sh
#
# Launch the nonlinear-case UIDD hyperparameter sensitivity sweep without
# modifying the original training/evaluation code.
#
# Defaults use 4 GPUs with 2 processes per GPU:
# sh run_uidd_sensitivity.sh
#
# Foreground run:
# sh run_uidd_sensitivity.sh --foreground
#
# Common overrides:
# SEEDS="0 1 1... |
9e59bdab55f6a48992f760365191d153c66bdd56738e5b0443df05c2d5f4e417 | Shell | 2,618 | 74 | #!/bin/bash
# -----------------------------------------------------------------------------
# MIT License
#
# Copyright (c) 2025 OpenIoT Research Unit (Fondazione Bruno Kessler)
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "... |
47e08474d4524844a264cd29739f7ce24e579284a27af88b4e33da2180df832e | Shell | 2,763 | 110 | #!/bin/sh
set -u
SCRIPT_DIR="$(CDPATH= cd -- "$(dirname -- "$0")" && pwd)"
cd "$SCRIPT_DIR"
GPU_ID1=3
GPU_ID2=5
GPU_ID3=6
KAPPA=0.8
DTS="0.01 0.005"
SEEDS="0 1 12 123 1234"
mkdir -p running_log
run_model() {
label="$1"
model_name="$2"
gpu_id="$3"
dt="$4"
seed="$5"
log_file="$6"
{
echo "===== ${... |
603b1edc5f96bd3318996ba037fc209f9c8087ac0234c7b650d6043d55546f99 | Shell | 3,001 | 84 | #!/bin/bash
abort() {
echo >&2 '
***************
*** ABORTED ***
***************
'
echo "Test failure" >&2
exit 1
}
function realpath () {
python -c "import os; print(os.path.realpath('${1}'))"
}
trap 'abort' 0
set -eu
cargo check
test_dir=/tmp/scratch
mkdir -p ${test_dir}
test_file=/tmp/scratch/... |
8e399bf02de27ca22440ef5e2eee80ddabfd25cbba34702bab559d6f4df936db | Shell | 3,099 | 133 | #!/bin/bash
usage() {
cat << EOF
Usage: batch-dl+direct [-h] [-c n_cpu] [-g n_GPU] [-b] [-m model_file] SRC_DIR DST_DIR
Batch processing using DL+DiReCT (with --bet), with N parallel jobs on CPU and GPU.
SRC_DIR is a directory with data to process, each subject should be in a separate subdirectory (with a T1.nii.gz in... |
68081a290e1c331f4b59dac4b68221b67bec5f7e2aa8ca0c7ace3bd6bda616e9 | Shell | 3,177 | 108 | #!/bin/sh
set -u
SCRIPT_DIR="$(CDPATH= cd -- "$(dirname -- "$0")" && pwd)"
cd "$SCRIPT_DIR"
DT="${DT:-0.01}"
KAPPA="${KAPPA:-0.8}"
SEEDS="${SEEDS:-0 1 12 123 1234}"
MODELS="${MODELS:-HD2 Onsager}"
EVAL_GPU="${EVAL_GPU:-6}"
NUM_TRAJS="${NUM_TRAJS:-1000}"
SOLVE_SUBSTEPS="${SOLVE_SUBSTEPS:-10}"
OUT_NAME="${OUT_NAME:-mm... |
a328fcef8f64d264e7b5dbf629b84ec4dbdc6bc318eb0e084a2f40bda12cc93c | Shell | 3,307 | 115 | #!/bin/bash -e
#
# Helper script to run clang-tidy on the codebase.
#
# Parse any input args.
build_dir=build-tidy
num_jobs=$(( $( command -v nproc > /dev/null && nproc || sysctl -n hw.physicalcpu ) / 2 ))
apply_fixits=
cache_dir=
type=
preset=
source_filter=
while getopts "j:B:fc:t:p:" opt; do
case $opt in
j) #... |
228b5bbe7f0d85630c985145e329a5f3182abddbc5049ca8fc3e991d0c9a1853 | Shell | 3,358 | 118 | #!/usr/bin/env bash
# Pre-pull AIND ephys pipeline containers into a Nextflow Singularity cache dir
#
# Usage:
# pull_aind_images.sh [--cache CACHE_DIR] [--tag si-X.Y.Z] [--sorter SORTER]
#
# Defaults:
# --cache : $NXF_SINGULARITY_CACHEDIR
# --tag : resolved from pipeline/capsule_versions.env (SPIKEINTERFAC... |
f6e1d1adb3ec57975da207ea6d578e1683bf938c53cb7a4aeb6cbe78b9c4cc6c | Shell | 3,384 | 119 | #!/usr/bin/env bash
# Pre-pull AIND ephys pipeline containers into a Nextflow Singularity cache dir
#
# Usage:
# pull_aind_images.sh [--cache CACHE_DIR] [--tag si-X.Y.Z] [--sorter SORTER]
#
# Defaults:
# --cache : $NXF_APPTAINER_CACHEDIR
# --tag : resolved from pipeline/capsule_versions.env (SPIKEINTERFACE_... |
4374b49afa6c4e0b849be57a497fab108a6b7590d7ea2baaa79ce14184f163b6 | Shell | 3,391 | 87 | #!/bin/bash
#SBATCH -n 32
#SBATCH -t 3-00:00
#SBATCH -N 1
#SBATCH -o %x_%j.o
#SBATCH -e %x_%j.e
#SBATCH --mem=128G
hostname
####################################
## for aggregated density plotting, i want to make a single hic file... |
d88c72ef8be16c6e8d6540e74893fbd9874c5eb9abd7646dd22913166194f906 | Shell | 3,476 | 123 | #!/bin/sh
set -u
SCRIPT_DIR="$(CDPATH= cd -- "$(dirname -- "$0")" && pwd)"
cd "$SCRIPT_DIR"
GPU_ID1="${GPU_ID1:-2}"
GPU_ID2="${GPU_ID2:-2}"
KAPPA="${KAPPA:-0.8}"
DTS="${DTS:-0.01}"
SEEDS="${SEEDS:-0 1 12 123 1234}"
BATCH_SIZE="${BATCH_SIZE:-100000}"
LEARNING_RATE="${LEARNING_RATE:-5e-4}"
NUM_EPOCHS="${NUM_EPOCHS:-6... |
d039c0257f21c682f09a0b7d2acf938a5055046880610a6547b2465b293a7be3 | Shell | 3,687 | 100 | #!/usr/bin/env bash
set -euo pipefail
source config/project_config.sh
BATCH_ID=${1:?Usage: bash scripts/02_run_batch.sh <batch_id, e.g. 1>}
mkdir -p rawdata fastq clean qc bam logs tmp
check_disk_space() {
local free_gb
free_gb=$(df -BG . | awk 'NR==2 {gsub("G","",$4); print $4}')
echo "Available disk: ${free_g... |
8e97e8d7864db91f24c6895b562d0a5d1312e268819f78301dd583a7435d655e | Shell | 3,841 | 109 | #!/bin/sh
#
# Train OnsagerReg with L2 and Sobolev regularization (two branches, in
# parallel on the same GPU; up to 2 python processes at any time), then
# evaluate both via evaluate_mmd.py. Self-backgrounds via nohup so a plain
# `sh run_reg.sh` returns to the prompt immediately.
#
# Override defaults via env vars, ... |
31521d3560a40f901b33e31e6648426d5adca1e2a14002bc0040dfb972480bba | Shell | 3,941 | 111 | #!/bin/bash
# Usage information
display_usage() {
echo "***************************************************************************************"
echo "Script to take bias corrected, eroded, skull mask and apply it to MEMPRAGE to remove EEG artifact."
echo "**************************************************... |
74179344ffb97905df7a5a3f8763a13972706f4a0051626bd1e53c670131f52e | Shell | 4,500 | 123 | #!/bin/sh
#
# Train OnsagerReg with L2 and Sobolev regularization (two branches, one per
# GPU), then
# evaluate both via evaluate_mmd.py. Self-backgrounds via nohup so a plain
# `sh run_reg.sh` returns to the prompt immediately.
#
# Override defaults via env vars, e.g.
# GPU_ID_L2=6 GPU_ID_SOB=7 SEEDS="1 12" sh run_... |
6dfffcc49f82f9c15bae2ff394344c2514945da6b4e1bf4e5ef5b0ba68cf852c | Shell | 4,699 | 157 | #!/bin/bash
usage() {
cat << EOF
Usage: dl+direct [-h] [-s subject] [-b [-i inv2_file]] [-n] [-m model_file] [-k] T1_FILE OUTPUT_DIR
Process T1_FILE (nifti) with dl+direct and put results into OUTPUT_DIR.
Input is expected to be a skull-stripped T1w MRI. You may specify --bet to remove
the skull (using hd-bet).
optio... |
cc769659afe2dd467f7a766640cf314d6e75d84d3fdcbcacb3e6decffb5c0da4 | Shell | 6,419 | 160 | #!/bin/bash
#SBATCH -n 32
#SBATCH -t 3-00:00
#SBATCH -N 1
#SBATCH -o %x_%j.o
#SBATCH -e %x_%j.e
#SBATCH --mem=128G
hostname
####################################
#<<DIGEST
module load Mambaforge
source activate CHiC_2024
FASTA=/Use... |
c80ab740a3a7cae19a95c5602976463d1ac9fbc205277f67fff390ba20eb1c6f | Shell | 6,852 | 155 | #!/bin/bash
# Integration tests for Dorado Correct.
set -ex
set -o pipefail
if [[ $# -lt 1 ]]; then
echo "Usage: $0 <dorado executable>"
exit 1
fi
# CLI options.
test_dir=$(dirname $0)
dorado_bin=$(cd "$(dirname $1)"; pwd -P)/$(basename $1)
cli_out_dir="$2"
# Test data directory.
data_dir=$test_dir/data
#... |
702d4e28361bfa8cf3d120b0ca32a691627971437ae284c24ac184c861938bd9 | Shell | 12,003 | 332 | #!/bin/bash
set -ex
set -o pipefail
if [[ $# -lt 1 ]]; then
echo "Usage: $0 <dorado executable>"
exit 1
fi
test_dir=$(dirname $0)
# Main arguments
dorado_bin=$(cd "$(dirname $1)"; pwd -P)/$(basename $1)
# Test on a tempdir to shorted filepaths which can cause issues on windows
TMPDIR="$(mktemp -d 2>/dev/nu... |
adc1a5924ee1e7b4d27b8a678117791de8197f91e08cf10ef625ad5fc4b6d005 | Shell | 15,730 | 385 | #!/bin/bash
# Test expected output structure from the dorado binary execution.
set -ex
set -o pipefail
if [[ $# -lt 1 ]]; then
echo "Usage: $0 <dorado executable> [model] [batch size]"
exit 1
fi
test_dir=$(dirname $0)
# Main arguments
dorado_bin=$(cd "$(dirname $1)"; pwd -P)/$(basename $1)
model=${2:-"hac"... |
c65fdbc16d8488af61cef003da400bf5ad2e0eeb11bcb68fb0ebc806a0fdc2e9 | Shell | 43,299 | 1,168 | #!/bin/bash
# ================================================================================
# Modkit Compilation Script for macOS (Apple Silicon)
# ================================================================================
# This script automates the compilation of Oxford
# Nanopore's modkit bioinformatics to... |
58377ee2987e17c8b7467cac24ffc160ec5a0f81352faf45bcc46aa6f3291859 | Shell | 49,884 | 1,006 | #!/bin/bash
# Test expected log output from the dorado binary execution.
set -ex
set -o pipefail
if [[ $# -lt 1 ]]; then
echo "Usage: $0 <dorado executable> [5k model] [batch size] [5k v43 model] [rna004 model] [model speed] [model version]"
exit 1
fi
test_dir=$(dirname $0)
dorado_bin=$(cd "$(dirname $1)"; ... |
eefcfeac2c0a53e6c0d512fc1d8ba30dbd9b9a04583c23c8fe4960852d8b6fb4 | Text | 48 | 2 | # Zebrafish-pituitary-blood-flow
For manuscript
|
7ed12813d9d4efab72ce2d01c9b2a489e6ba9a2762ba9344692f76630d9c5821 | Text | 81 | 3 | # aind-capsule-template
Basic structure of a capsule to be customized as needed. |
d6cc15ab2ff6a2080b92c4fa41c7a5a87f7f392fcfc5d00c5529108bef2f3f11 | Text | 118 | 2 | # Neural-manifold-for-short-term-prediction
This code is used for short-term prediction simulation of neural signals.
|
d21fee618ea016eb81911527677988849f9e82b71bad0b5a0e9dd56416c21ba6 | Text | 131 | 2 | # RRL-Momentum-Beds
Repository of 3D printed beds compatible with the Magnetic Insight Momentum magnetic particle imaging scanner.
|
7156d1a9a93c6aff3c23e89ef4af0793f6f3f7d707c60732ff9714c687722bda | Text | 204 | 2 | # capture-hic-imprinting
Scripts "Allele-specific chromatin architecture shapes imprinted domains and coordinates a distal enhancer and antisense transcription at the Mest-Copg2 domain" (Bae et al. 2026)
|
faca88083fc540e23cf38feed548943111e3dd45bb4280094f279b67b5435dbd | Text | 244 | 2 | # COVID-19
IC50 is a measure of the effectiveness of a substance in inhibiting a specific biological or biochemical function. For COVID-19, predicting the IC50 value of compounds can help in understanding their potential as therapeutic agents.
|
5e33a2a7504db0506fd9c8a68aeec4afb3b04f5efbec6e637f152471bbe1645f | Text | 338 | 2 | # Prefrontal-and-auditory-cortex-compete-in-learning
Data and code associated with the manuscript, “Neural competition between prefrontal and auditory cortex constrains novel sound strategy learning” by Kai Lu, Kelvin T. Wong, Chengcheng J. Yang, Lin N. Zhou, Yike T. Shi, Maya L. Costello, Robert C. Liu. Please cite th... |
77160139e975efecbca0df6a9ac4dd244321ad79ecd33e32d37203b9a5648360 | Text | 539 | 12 | # pattern_quality
Data and codes used in Palm et al. (2026) "A Quality Measure for Repeating Multiple-Unit Spike Patterns"
## Setting up the environment
- We recommend using Miniforge (https://github.com/conda-forge/miniforge) to manage virtual environments.
- Create a dedicated virtual environment
- > conda create ... |
527fbbded57ce5d5ddc0b75342695bdc00fdd83795de6d6fe143810985f97268 | Text | 589 | 7 | # NN-Assisted Image Analysis for Quantifying Intracellular Trypanosoma cruzi Infection
Repository of the scripts used for the publication "NN-Assisted Image Analysis for Quantifying Intracellular Trypanosoma cruzi Infection", at the Signaling and Adaptive Mechanisms in Trypanosomatids Laboratory.
Google colab: https:/... |
1c74ec6d8556c0d5ed2f57b5664a5d448d8dfd0cfae88e5ee2f0f17f1ee73ca4 | Text | 637 | 16 | Acquisition2P_class
===================
For managing 2P imaging datasets from preprocessing to activity trace extraction
Includes three classes (Acquisition2P, selectRoisGui, acq2pJobProcessor), associated methods,
and code specifically pertaining to their use.
Using the software in this repository also requires mul... |
447030950004cd1fc19085162c9c9ac075b231b898786bb03a0036b2b120ee34 | Text | 649 | 7 | This repo contains basic code to train multi-region data-constrained recurrent neural network (RNN) models and perform current-based decomposition (CURBD).
For details, see: Perich MG, Arit C, Soares S, Young ME, Mosher CP, Minxha J, Carter E, Rutishauser U, Rudebeck PH, Harvey CD, Rajan K. Inferring brain-wide intera... |
c86c80f7025b6a4b8459b22778bdfa367f97384c2377ba68ae1be8b61598384c | Text | 717 | 15 | # neuron_microgravity
Python files used in the following paper: [Gontier, C., Kalinski, L., Striebel, J., Sturm, M., Meerholz, Z., Schunk, S., ... & Liemersdorf, C. (2024). A computational model of altered neuronal activity in altered gravity. bioRxiv.](https://www.biorxiv.org/content/10.1101/2024.07.30.605832v1)
## ... |
4aa0c6e29f6a2adcbf18b7d566909bdcc1f382b88b882d3e4668aca330b330ff | Text | 795 | 18 | # BlinkingSimulator
A realistic simulation tool to create microscopy movies of blinking emitters:
- creates different patterns: microtubules, mitochondria, random, filament, circular
- realistic noise by using realistic sCMOS model: gain, variance and offset map
- suitable to create large training and test datasets... |
37c1475727463b8a5ae9eeefa438862a89d5632c67977f2a30c09715c968471c | Text | 810 | 23 | # Quality Control Collector for AIND ephys pipeline
## aind-ephys-qc-collector
### Description
This capsule is designed to compute collect all `aind-data-schema QualityControl` JSON files generated for different streams and aggregate them into a single `quality_control.json`
### Inputs
The `data/` folder must incl... |
25847375f4f449bd1b99172b3ca129be5748870e53ff2206b13f6cf6139c2861 | Text | 989 | 14 | # Microvilli_ER_vEM
Volume electron microscopy (vEM) analysis of microvilli and ER across three regions of interest (ROIs).
Alexander Ludwig – Low Kay En
<img width="612" height="504" alt="image" src="https://github.com/user-attachments/assets/ba211b1b-53f4-4cb9-b52f-cca716da0267" />
## Contents
- **Scripts/Prepro... |
9c3e52c73dd5ddc6183018809514b4e7394b39565723b6c4409e94a4f62d39b0 | Text | 1,075 | 16 | Hi there.
These codes have been developed to analyse FFN200 data acquired with a two-photon microscope in acute brain slices.
A more in-depth description can be obtained from the following published paper:
Below is a simple description of each code:
1-2-3. Using FIJI and Python3, these codes will correct for the x,y,... |
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