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<!DOCTYPE html>
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<title>Brain Image Library: Computing and Visualization</title>
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<h1 id="The-BIL-Analysis-Ecosystem" data-id="The-BIL-Analysis-Ecosystem" style="">
<a class="anchor hidden-xs" href="#The-BIL-Analysis-Ecosystem" title="The-BIL-Analysis-Ecosystem">
<span class="octicon octicon-link"></span>
</a>
<img src="https://i.imgur.com/GLp06Vi.png" width="70">
<span>The BIL Analysis Ecosystem</span>
</h1>
<h2 id="How-to-connect-to-the-BIL-Analysis-Ecosystem" data-id="How-to-connect-to-the-BIL-Analysis-Ecosystem"
style="">
<a class="anchor hidden-xs" href="#How-to-connect-to-the-BIL-Analysis-Ecosystem"
title="How-to-connect-to-the-BIL-Analysis-Ecosystem">
<span class="octicon octicon-link"></span>
</a>
<span>How to connect to the BIL Analysis Ecosystem</span>
</h2>
<h3 id="Connect-via-Terminal" data-id="Connect-via-Terminal" style="">
<a class="anchor hidden-xs" href="#Connect-via-Terminal" title="Connect-via-Terminal">
<span class="octicon octicon-link"></span>
</a>
<span>Connect via Terminal</span>
</h3>
<h3 id="SSH" data-id="SSH" style="">
<a class="anchor hidden-xs" href="#SSH" title="SSH">
<span class="octicon octicon-link"></span>
</a>
<span>SSH</span>
</h3>
<p><span>You can connect to BIL Analysis ecosystem resources with an ssh client from your local machine using your PSC credentials.</span>
</p>
<p><span>You must install SSH client software on your local machine, but free ssh clients for
Macs, Windows and Unix are available. Popular ssh clients (GUI) include PuTTY for Windows
and Cyberduck for Macs. A command line version of ssh is installed on Macs by default
and you can use the Terminal application if you prefer. You can also check with your university
to see if there is an ssh client that they recommend.
</span></p>
<p><span>To use ssh to connect to the BIL Analysis Ecosystem:</span></p>
<pre><code>ssh [email protected]</code></pre>
<p><span>Everyone who requests a BIL account has access to the login node using their BIL Username
and Password. The login node is not intended for heavy computation or visualization, but rather
to provide convenient shell access to BIL data and enable interactive and batch use of the BIL
Analysis Ecosystem. The BIL computational cluster provides a suitable resource for both
computation and visualization.
</span></p>
<h4 id="Workshop-VM" data-id="Workshop-VM">
<a class="anchor hidden-xs" href="#Workshop-VM" title="Workshop-VM">
<span class="octicon octicon-link"></span>
</a>
<h2 id="Interactive-Apps" data-id="Interactive-Apps" style=""><a class="anchor hidden-xs"
href="#Interactive-Apps"
title="Interactive-Apps"><span
class="octicon octicon-link"></span></a><span>Interactive Apps</span></h2>
<h3 id="OpenOnDemand" data-id="OpenOnDemand" style=""><a class="anchor hidden-xs" href="#OpenOnDemand"
title="OpenOnDemand"><span
class="octicon octicon-link"></span></a><span>OpenOnDemand</span></h3>
<p><span>The OpenOnDemand (OOD) interface allows you to connect to the BIL Analysis Ecosystem through the web browser. You can submit and manage jobs, move or create files, or use the apps such as Jupyter Notebook.</span>
</p>
<p><span>To connect to the BIL Analysis Ecosystem via Open OnDemand</span></p>
<ol>
<li>
<p><span>In your web broswer, go to </span><code>https://ondemand.bil.psc.edu</code></p>
</li>
<li>
<p><span>Enter your </span><a href="https://hackmd.io/lXd3fXcNSg-odAVC8APRuQ" target="_blank"
rel="noopener"><span>PSC username and password</span></a><br>
<img src="https://i.imgur.com/ARpR80E.png" alt="" loading="lazy"></p>
</li>
<li>
<p><span>From the OOD dashboard, pictured below, you will see the top menu bar where you can manage file, jobs, or select the apps to use.</span>
</p>
</li>
</ol>
<p><img src="https://i.imgur.com/ZKeTVXG.png" alt="" loading="lazy"></p><h4 id="Manage-files"
data-id="Manage-files"><a
class="anchor hidden-xs" href="#Manage-files" title="Manage-files"><span
class="octicon octicon-link"></span></a><span>Manage files</span></h4>
<p>
<span>From the OOD dashboard, you can create, edit, or move files. Select the </span><code>Files</code><span> option from the top menu bar, then the </span><code>Home</code><span> which will navigate to your home directory at </span><code>/bil/users/</code><span>. From here, you will have the following options:</span>
</p>
<ul>
<li><code>Go To…</code><span>: Navigate to a specified folder</span></li>
<li><code>Open in Terminal</code><span>: Opens the active folder in a terminal session (new tab)</span>
</li>
<li><code>New File</code><span>: Creates a new file in the active folder</span></li>
<li><code>New Dir</code><span>: Creates a new folder in the active folder</span></li>
<li>
<code>Upload</code><span>: Select files from your local machine to upload to the active folder</span>
</li>
<li><code>Show Dotfiles</code><span>: Reveals hidden files</span></li>
<li><code>Show Owner/Mode</code><span>: Shows ownership and permission information</span></li>
<li><code>View</code><span>: Shows file contents inside the current tab</span></li>
<li><code>Edit</code><span>: Opens a file editor in a new tab</span></li>
<li><code>Rename/Move</code><span>: Gives a file a new path and/or name</span></li>
<li><code>Download</code><span>: Downloads the file or folder to your local machine</span></li>
<li><code>Copy</code><span>: Copies selected files to the clipboard</span></li>
<li><code>Paste</code><span>: Pastes files from the clipboard</span></li>
<li><code>(Un)Select All</code><span>: Select or unselect all files/folders</span></li>
<li><code>Delete</code><span>: Deletes selected files/folders</span></li>
</ul>
<h4 id="Manage-Jobs" data-id="Manage-Jobs"><a class="anchor hidden-xs" href="#Manage-Jobs"
title="Manage-Jobs"><span class="octicon octicon-link"></span></a><span>Manage Jobs</span>
</h4>
<p>
<span>From the OOD dashboard, you can create, submit, and edit jobs. Select the </span><code>Jobs</code><span> option from the top menu bar, then </span><code>Job
composer</code><span> which will take you to the job composer dashboard. From here, you will have the following options:</span>
</p>
<ul>
<li><span>Create a new job script</span></li>
<li><span>Edit job scripts</span></li>
<li><span>Submit a job</span></li>
</ul>
<p><span>When you first visit to this page, you'll go through a helpful tutorial. The buttons do the following:</span>
</p>
<ul>
<li><code>New Job</code><span>: Create a new job</span>
<ul>
<li><code>From Default Template</code><span>: Uses system defaults to create a job that you can then edit.</span>
</li>
<li><code>From Specified Path</code><span>: Creates a job from a specific job script.</span>
</li>
<li><code>From Selected
Job</code><span>: Creates a new job that is a copy of the selected job.</span></li>
</ul>
</li>
<li><code>Edit Files</code><span>: Opens the project folder in a new File Explorer tab and allows you to edit the files within it.</span>
</li>
<li><code>Job Options</code><span>: Allows you to edit the Name, Cluster, Job Script, and Account of a job.</span>
</li>
<li><code>Open
Terminal</code><span>: Opens a terminal session in a new tab at the project folder.</span></li>
<li><code>Submit</code><span>: Submits the selected job.</span></li>
<li><code>Stop</code><span>: Stops the selected job if it was already submitted.</span></li>
<li><code>Delete</code><span>: Delete the selected job.</span></li>
</ul>
<h4 id="Jupyter-Notebook" data-id="Jupyter-Notebook"><a class="anchor hidden-xs" href="#Jupyter-Notebook"
title="Jupyter-Notebook"><span
class="octicon octicon-link"></span></a><span>Jupyter Notebook</span></h4>
<p><span>From the OOD dashboard you can launch a Jupyter Notebook server on one or more nodes.</span></p>
<ul>
<li><span>Select the </span><code>Apps</code><span> option from the top menu bar, then </span><code>Jupyter
Notebook</code><span> which will take you to the page to set up your Jupyer Notebook session.</span>
</li>
<li><span>From here, you will specify the timelimit, number of nodes to use. Use the Extra Slurm Args field to specify the number of cores or number of GPUs you want. Use the Extra Jupyter Args field to pass arguments to your Jupyter notebook.</span>
</li>
<li><span>Select </span><code>Launch</code><span> to begin your Jupyter Notebook session.</span></li>
<li><span>You will be taken to the dashboard for your interactive sessions. It may take some time for your resources to become available. When your session starts, select the blue "Connect to Jupyter"</span>
</li>
<li>
<span>A new window running Jupyter Hub will open where you can being your Jupyter Notebook session.</span>
</li>
<li><span>For instructions on using Jupyter Notebook, see the </span><a
href="https://jupyter-notebook.readthedocs.io/en/stable/notebook.html" target="_blank"
rel="noopener"><span>official documentation</span></a><span>.</span></li>
</ul>
<h2 id="Software-Modules" data-id="Software-Modules" style=""><a class="anchor hidden-xs"
href="#Software-Modules"
title="Software-Modules"><span
class="octicon octicon-link"></span></a><span>Software Modules</span></h2>
<h3 id="LMOD" data-id="LMOD" style=""><a class="anchor hidden-xs" href="#LMOD" title="LMOD"><span
class="octicon octicon-link"></span></a><span>LMOD</span></h3><img
src="https://i.imgur.com/TiNg8y8.png" width="25%">
<p><span>Lmod is a Lua based module system that easily handles the MODULEPATH Hierarchical problem. Environment Modules provide a convenient way to dynamically change the users' environment through modulefiles.</span>
</p>
<p><span>In a nutshell, we use LMOD to manage software that can be used in the VM as well as the large memory nodes. Software available as modules should be accessible on both resources.</span>
</p>
<p><span>This document only lists a few commands. For complete documentation click </span><a
href="https://lmod.readthedocs.io/en/latest/010_user.html" target="_blank"
rel="noopener"><span>here</span></a><span>.</span></p>
<div class="alert alert-info">
<p><img class="emoji" alt=":bulb:"
src="https://cdn.jsdelivr.net/npm/@hackmd/[email protected]/dist/images/basic/bulb.png"><span> If you want us to install a piece of software in our resources, then please remember to submit software installation requests to </span><code>[email protected]</code><span>.</span>
</p>
</div>
<h3 id="Available-software-modules" data-id="Available-software-modules" style=""><a
class="anchor hidden-xs" href="#Available-software-modules" title="Available-software-modules"><span
class="octicon octicon-link"></span></a><span>Available software modules</span></h3>
<p><span>To list all available software modules use the command</span></p>
<pre><code>module avail
</code></pre>
<p><span>For example</span></p>
<pre><code>module avail
-------------- /bil/modulefiles ---------------
anaconda/3.2019.7
anaconda3/4.10.1
aspera/3.9.6(default)
bcftools/1.9(default)
bioformats/6.0.1
bioformats/6.1.1
bioformats/6.4.0
bioformats/6.5.1
bioformats/6.6.1(default)
bioformats2raw/0.2.4(default)
c-blosc/1.19.0(default)
dust/0.5.4
ffmpeg/20210611
</code></pre>
<p><span>The command above will list all available software.</span></p>
<div class="alert alert-info">
<p><img class="emoji" alt=":envelope:"
src="https://cdn.jsdelivr.net/npm/@hackmd/[email protected]/dist/images/basic/envelope.png"><span> Cannot find the software you need to explore the collections? Please send a request to </span><code>[email protected]</code><span>.</span>
</p>
</div>
<h3 id="Software-versions" data-id="Software-versions" style=""><a class="anchor hidden-xs"
href="#Software-versions"
title="Software-versions"><span
class="octicon octicon-link"></span></a><span>Software versions</span></h3>
<p><span>To list information about specific modules use the command</span></p>
<pre><code>module avail <package-name>
</code></pre>
<p><span>For example, you can view the two versions of MatLab available</span></p>
<pre><code>module avail matlab
-------------- /bil/modulefiles ---------------
matlab/2019a matlab/2021a
</code></pre>
<h4 id="Listing-useful-information" data-id="Listing-useful-information"><a class="anchor hidden-xs"
href="#Listing-useful-information"
title="Listing-useful-information"><span
class="octicon octicon-link"></span></a><span>Listing useful information</span></h4>
<p><span>To list useful info about a module use the command</span></p>
<pre><code>module help <package-name>
</code></pre>
<p><span>For example,</span></p>
<pre><code>module help matlab
----------- Module Specific Help for 'matlab/2021a' ---------------
Matlab 2021a
------------
To enable, first load the following required modules (via module load command):
module load matlab/2021a
For a full list of binaries included in this module, type
module what-is matlab/2021a
</code></pre>
<h3 id="Loading-modules" data-id="Loading-modules" style=""><a class="anchor hidden-xs"
href="#Loading-modules"
title="Loading-modules"><span
class="octicon octicon-link"></span></a><span>Loading modules</span></h3>
<p><span>To load a module use the command</span></p>
<pre><code>module load <package-name>
</code></pre>
<p><span>For example,</span></p>
<pre><code>module load matlab/2021a
</code></pre>
<p><span>Running the command above will make the matlab binary available in the current session</span></p>
<pre><code>which matlab
/bil/packages/matlab/R2021a/bin/matlab
</code></pre>
<p>
<span>In this example, you can simply type </span><code>matlab</code><span> to start the Matlab engine</span>
</p>
<pre><code>matlab -nodesktop
MATLAB is selecting SOFTWARE OPENGL rendering.
< M A T L A B (R) >
Copyright 1984-2021 The MathWorks, Inc.
R2021a Update 5 (9.10.0.1739362) 64-bit (glnxa64)
August 9, 2021
To get started, type doc.
For product information, visit www.mathworks.com.
>>
</code></pre>
<h3 id="Loading-a-specific-version-of-a-module" data-id="Loading-a-specific-version-of-a-module" style=""><a
class="anchor hidden-xs" href="#Loading-a-specific-version-of-a-module"
title="Loading-a-specific-version-of-a-module"><span class="octicon octicon-link"></span></a><span>Loading a specific version of a module</span>
</h3>
<p><span>There are times when there are multiple versions of the same same software.</span></p>
<p><span>For example,</span></p>
<pre><code>module avail bioformats
---------------------- /bil/modulefiles ----------------------
bioformats/6.0.1 bioformats/6.7.0
bioformats/6.1.1 bioformats/6.8.0(default)
bioformats/6.4.0 bioformats2raw/0.2.4
bioformats/6.5.1 bioformats2raw/0.3.0(default)
bioformats/6.6.1
</code></pre>
<p><span>If you wish to load a specific version of a package use the command</span></p>
<pre><code>module load <package>/<version>
</code></pre>
<p><span>For example,</span></p>
<pre><code>module load bioformats/6.4.0
</code></pre>
<h3 id="Listing-loaded-modules" data-id="Listing-loaded-modules" style=""><a class="anchor hidden-xs"
href="#Listing-loaded-modules"
title="Listing-loaded-modules"><span
class="octicon octicon-link"></span></a><span>Listing loaded modules</span></h3>
<p><span>To list the loaded modules use the command</span></p>
<pre><code>module list
</code></pre>
<p><span>For example,</span></p>
<pre><code>module list
Currently Loaded Modulefiles:
1) matlab/2021a
</code></pre>
<h3 id="Unload-module" data-id="Unload-module" style=""><a class="anchor hidden-xs" href="#Unload-module"
title="Unload-module"><span
class="octicon octicon-link"></span></a><span>Unload module</span></h3>
<p><span>To load a module use the command</span></p>
<pre><code>module unload <package-name>
</code></pre>
<p><span>for example</span></p>
<pre><code>module unload matlab/2021a
</code></pre>
<h3 id="Using-modules-on-scripts" data-id="Using-modules-on-scripts" style=""><a class="anchor hidden-xs"
href="#Using-modules-on-scripts"
title="Using-modules-on-scripts"><span
class="octicon octicon-link"></span></a><span>Using modules on scripts</span></h3>
<p><span>When building scripts that are using more than one tool available as modules, simply type the module command for each tool</span>
</p>
<pre><code class="hljs"><div class="wrapper"><div class="gutter linenumber"><span></span>
<span></span>
<span></span>
<span></span></div><div class="code">#!/bin/bash
module load matlab/2021a
module load bioformats
</div></div></code></pre>
<h2 id="Job-management" data-id="Job-management" style=""><a class="anchor hidden-xs" href="#Job-management"
title="Job-management"><span
class="octicon octicon-link"></span></a><span>Job management</span></h2>
<h3 id="SLURM" data-id="SLURM" style=""><a class="anchor hidden-xs" href="#SLURM" title="SLURM"><span
class="octicon octicon-link"></span></a><span>SLURM</span></h3>
<p><img src="https://i.imgur.com/3gPmu1r.png" alt="" loading="lazy"></p>
<p><a href="https://slurm.schedmd.com/documentation.html" target="_blank" rel="noopener"><span>Slurm</span></a><span> is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for large and small Linux clusters.</span>
</p>
<p><span>This document only lists a few commands. For complete documentation click </span><a
href="https://slurm.schedmd.com/documentation.html" target="_blank" rel="noopener"><span>here</span></a><span>.</span>
</p>
<h3 id="sinfo" data-id="sinfo" style=""><a class="anchor hidden-xs" href="#sinfo" title="sinfo"><span
class="octicon octicon-link"></span></a><span>sinfo</span></h3>
<pre><code>sinfo - View information about Slurm nodes and partitions.
SYNOPSIS
sinfo [OPTIONS...]
</code></pre>
<p><span>For example</span></p>
<pre><code>sinfo -p compute
</code></pre>
<h3 id="squeue" data-id="squeue" style=""><a class="anchor hidden-xs" href="#squeue" title="squeue"><span
class="octicon octicon-link"></span></a><span>squeue</span></h3>
<pre><code>squeue - view information about jobs located in the Slurm scheduling queue.
SYNOPSIS
squeue [OPTIONS...]
</code></pre>
<p><span>For example</span></p>
<pre><code>squeue -u icaoberg
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
14243 compute script.s icaoberg R 15:34 1 l001
</code></pre>
<h3 id="scontrol" data-id="scontrol" style=""><a class="anchor hidden-xs" href="#scontrol" title="scontrol"><span
class="octicon octicon-link"></span></a><span>scontrol</span></h3>
<pre><code>scontrol - view or modify Slurm configuration and state.
SYNOPSIS
scontrol [OPTIONS...] [COMMAND...]
</code></pre>
<p><span>As a regular user you can view information about the nodes and jobs but won't be able to modify them.</span>
</p><h4 id="Check-available-memory" data-id="Check-available-memory"><a class="anchor hidden-xs"
href="#Check-available-memory"
title="Check-available-memory"><span
class="octicon octicon-link"></span></a><span>Check available memory</span></h4>
<p><span>The view information about the nodes, including information about memory, use the command</span>
</p>
<pre><code>scontrol show nodes
</code></pre>
<p>
<span>To view information about a specific node, use the node name to print this information. For example</span>
</p>
<pre><code>scontrol show nodes l002
NodeName=l002 Arch=x86_64 CoresPerSocket=20
CPUAlloc=0 CPUTot=80 CPULoad=0.03
AvailableFeatures=(null)
ActiveFeatures=(null)
Gres=(null)
NodeAddr=l002 NodeHostName=l002 Version=18.08
OS=Linux 4.18.0-305.7.1.el8_4.x86_64 #1 SMP Tue Jun 29 21:55:12 UTC 2021
RealMemory=3000000 AllocMem=0 FreeMem=3090695 Sockets=4 Boards=1
State=IDLE ThreadsPerCore=1 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A
Partitions=compute
BootTime=2021-07-16T15:47:48 SlurmdStartTime=2021-08-03T20:58:25
CfgTRES=cpu=80,mem=3000000M,billing=80
AllocTRES=
CapWatts=n/a
CurrentWatts=0 LowestJoules=0 ConsumedJoules=0
ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s
</code></pre>
<p>
<span>Because there exists one partition, the you can run </span><code>sinfo</code><span> or </span><code>sinfo
-p compute</code><span> to gather basic information about this partition.</span></p>
<p><span>For example</span></p>
<pre><code>→ sinfo -p compute
PARTITION AVAIL TIMELIMIT NODES STATE NODELIST
compute* up infinite 8 idle l[001-008]
</code></pre>
<h4 id="sbatch" data-id="sbatch"><a class="anchor hidden-xs" href="#sbatch" title="sbatch"><span
class="octicon octicon-link"></span></a><span>sbatch</span></h4>
<pre><code>sbatch - Submit a batch script to Slurm.
SYNOPSIS
sbatch [OPTIONS(0)...] [ : [OPTIONS(N)...]] script(0) [args(0)...]
</code></pre>
<h4 id="interact" data-id="interact"><a class="anchor hidden-xs" href="#interact" title="interact"><span
class="octicon octicon-link"></span></a><span>interact</span></h4>
<p><span>The interact command is an in-house script for starting interactive sessions</span></p>
<pre><code>interact -h
Usage: interact [OPTIONS]
-d Turn on debugging information
--debug
--noconfig Do not process config files
-gpu Allocate 1 gpu in the GPU-shared partition
--gpu
--gres=<list> Specifies a comma delimited list of generic consumable
resources. e.g.: --gres=gpu:1
--mem=<MB> Real memory required per node in MegaBytes
-N Nodes Number of nodes
--nodes
-n NTasks Number of tasks (spread over all Nodes)
--ntasks-per-node=<ntasks> Number of tasks, 1 per core per node.
-p Partition Partition/queue you would like to run on
--partition
-R Reservation Reservation you would like to run on
--reservation
-t Time Set a limit on the total run time. Format include
mins, mins:secs, hours:mins:secs. e.g. 1:30:00
--time
-h Print this help message
-?
</code></pre>
<ul>
<li><span>At the moment, there only exists one partition named </span><code>compute</code><span>, so running</span>
</li>
</ul>
<pre><code>interact
</code></pre>
<p><span>or</span></p>
<pre><code>interact -p compute
</code></pre>
<ul>
<li><span>To specify the amount of memory use the option </span><code>--mem=<MB></code><span>. For example </span><code>interact
--mem=1Tb</code></li>
<li><span>This is a shared partition, if you wish to get all the resources in a compute node, use the option </span><code>--nodes</code><span>. For example </span><code>interact
-N
1</code><span>. Since this is a shared resource, please be considerate using this resource.</span>
</li>
</ul>
<h4 id="scancel" data-id="scancel"><a class="anchor hidden-xs" href="#scancel" title="scancel"><span
class="octicon octicon-link"></span></a><span>scancel</span></h4>
<pre><code>scancel - Used to signal jobs or job steps that are under the control of Slurm.
SYNOPSIS
scancel [OPTIONS...] [job_id[_array_id][.step_id]] [job_id[_array_id][.step_id]...]
</code></pre>
<p><span>There is no need to</span></p>
<ul>
<li><span>To cancel a specific job use the command </span><code>scancel <job_id></code><span>. For example </span><code>scancel
00001</code></li>
<li><span>To cancel all your running jobs use the command </span><code>scancel -u
<username></code><span>. For example </span><code>scancel -u icaoberg</code><span>.</span>
</li>
</ul>
<h3 id="Docker" data-id="Docker" style=""><a class="anchor hidden-xs" href="#Docker" title="Docker"><span
class="octicon octicon-link"></span></a><span>Docker</span></h3>
<p><span>Docker is not supported and it is not expected to be supported in the near future.</span></p><h4
id="uDocker" data-id="uDocker"><a class="anchor hidden-xs" href="#uDocker" title="uDocker"><span
class="octicon octicon-link"></span></a><span>uDocker</span></h4><img
src="https://github.com/indigo-dc/udocker/raw/master/docs/logo-small.png" width="25%">
<p><span>If you want to run a program/tool and not a service, then </span><a
href="https://github.com/indigo-dc/udocker" target="_blank"
rel="noopener"><span>uDocker</span></a><span> might be an option for you.</span></p>
<p><span>To install uDocker</span></p>
<pre><code>module load anaconda3/4.11.0
pip install --user udocker
</code></pre>
<p><span>or</span></p>
<pre><code>module load anaconda3/4.11.0
python -m venv .
source ./bin/activate
pip install udocker
</code></pre>
<p><span>For example,</span></p>
<pre><code>udocker pull jtduda/python-itk-sitk-ants:0.1.0
</code></pre>
<h3 id="Singularity" data-id="Singularity" style=""><a class="anchor hidden-xs" href="#Singularity"
title="Singularity"><span
class="octicon octicon-link"></span></a><span>Singularity</span></h3><h4 id="Building-containers"
data-id="Building-containers">
<a class="anchor hidden-xs" href="#Building-containers" title="Building-containers"><span
class="octicon octicon-link"></span></a><span>Building containers</span></h4>
<p><strong><span>If you have elevated privileges to run Singularity</span></strong><br>
<span>Make sure to run singularity builds as </span><code>sudo</code><span>, that's all that matters.</span>
</p>
<div class="alert alert-warning">
<p><img class="emoji" alt=":warning:"
src="https://cdn.jsdelivr.net/npm/@hackmd/[email protected]/dist/images/basic/warning.png"><span> If you are constantly building containers, then run</span>
</p>
<pre><code>singularity cache clean
</code></pre>
<p><span>often to clean cache.</span></p>
</div>
<p><strong><span>If you don't have elevated privileges</span></strong></p>
<p><span>This applies to all regular users including researchers. If you do not have elevated privileges, you can still build the images remotely.</span>
</p>
<p><span>Follow these steps to do so</span></p>
<ul>
<li><span>Create an account on </span><a href="http://SyLabs.io" target="_blank" rel="noopener"><span>SyLabs.io</span></a><span>.</span>
</li>
<li><span>Click </span><code>Access Tokens</code><span> on the top-right menu</span></li>
</ul>
<p><img src="https://i.imgur.com/ILAwB6T.png" alt="" loading="lazy"></p>
<ul>
<li><span>Click Create a </span><code>New Access Token</code></li>
</ul>
<p><img src="https://i.imgur.com/HlKCHjo.png" alt="" loading="lazy"></p>
<ul>
<li><span>Click </span><code>Copy token to Clipboard</code></li>
</ul>
<p><img src="https://i.imgur.com/ztbbC8B.png" alt="" loading="lazy"></p>
<ul>
<li><span>Login to the </span><code>workshop</code><span> VM and run the command</span></li>
</ul>
<pre><code>singularity remote login
</code></pre>
<ul>
<li><span>Paste the token and click </span><code>Enter</code><span>.</span></li>
</ul>
<p>
<span>Just make sure to use the </span><code>--remote</code><span> flag when running singularity build.</span>
</p>
<p><span>Check the </span><code>rbuild.sh</code><span> scripts in each repo for working examples.</span></p>
<div class="alert alert-warning">
<p><img class="emoji" alt=":warning:"
src="https://cdn.jsdelivr.net/npm/@hackmd/[email protected]/dist/images/basic/warning.png"><span> If you are constantly building containers remotely, make sure to erase them from your account to avoid running out of space.</span>
</p>
</div>
<p><span>To see a list of vetted containers built by PSC, click </span><a
href="https://github.com/pscedu/singularity" target="_blank"
rel="noopener"><span>here</span></a><span>.</span></p><h4 id="Example" data-id="Example"><a
class="anchor hidden-xs" href="#Example" title="Example"><span
class="octicon octicon-link"></span></a><span>Example</span></h4><img
src="https://camo.githubusercontent.com/d18f42e3f0fc2eb3d39084c23a19eaf5a65c25ed7d14fcef9c00c8176680fa95/68747470733a2f2f75706c6f61642e77696b696d656469612e6f72672f77696b6970656469612f636f6d6d6f6e732f382f38302f436f777361795f5479706963616c5f4f75747075742e706e67">
<p><span>You can find a Singularity definition file </span><a
href="https://github.com/pscedu/singularity-cowsay" target="_blank" rel="noopener"><span>here</span></a><span>. To build this image remotely run</span>
</p>
<pre><code>git clone https://github.com/pscedu/singularity-cowsay.git
cd 3.04
singularity build --remote cowsay.sif Singularity
</code></pre>
<p><span>after getting a token from </span><a href="http://SyLabs.io" target="_blank" rel="noopener"><span>SyLabs.io</span></a><span>.</span>
</p>
<h2 id="Other" data-id="Other" style=""><a class="anchor hidden-xs" href="#Other" title="Other"><span
class="octicon octicon-link"></span></a><span>Other</span></h2>
<h3 id="Installing-Miniconda" data-id="Installing-Miniconda" style=""><a class="anchor hidden-xs"
href="#Installing-Miniconda"
title="Installing-Miniconda"><span
class="octicon octicon-link"></span></a><span>Installing Miniconda</span></h3>
<p><img src="https://upload.wikimedia.org/wikipedia/commons/e/ea/Conda_logo.svg" width="50%"><br></p>
<p><span>There is nothing preventing you from installing a Conda distribution in your home directory, though this is not advised.</span>
</p>
<p><span>However if you need to, you might want to start with a Miniconda distribution</span></p>
<pre><code class="hljs"><div class="wrapper"><div class="gutter linenumber"><span></span>
<span></span></div><div class="code">wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash ./https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
</div></div></code></pre>
<p><span>and follow the instructions on screen.</span></p>
<div class="alert alert-info">
<p><img class="emoji" alt=":pencil:"
src="https://cdn.jsdelivr.net/npm/@hackmd/[email protected]/dist/images/basic/pencil.png"><span> If you use the default values in the Conda install, it will install in your home directory on </span><code>/bil/</code>
</p>
</div>
<h3 id="Using-Jupyter-Notebooks" data-id="Using-Jupyter-Notebooks" style=""><a class="anchor hidden-xs"
href="#Using-Jupyter-Notebooks"
title="Using-Jupyter-Notebooks"><span
class="octicon octicon-link"></span></a><span>Using Jupyter Notebooks</span></h3><h4
id="Loading-the-proper-module" data-id="Loading-the-proper-module"><a class="anchor hidden-xs"
href="#Loading-the-proper-module"
title="Loading-the-proper-module"><span
class="octicon octicon-link"></span></a><span>Loading the proper module</span></h4>
<p><span>Click the black terminal icon in the top left corner of your screen</span></p>
<p><img src="https://i.imgur.com/Um1L4Kj.png" alt="" loading="lazy"></p>
<p><span>When the terminal opens, type the following commands to load Fiji into your workspace.</span></p>
<pre><code>module load anaconda3
jupyter lab
</code></pre>
<p><span>Running the commands above will open a browser</span></p>
<p><img src="https://i.imgur.com/WJb8t6i.png" alt="" loading="lazy"></p>
<p><span>The Anaconda3 installation available in BIL infrastructure has access to commonly used packages used in data analytics but it also has a list of unique packages commonly used in neuroscience like</span>
</p>
<ul>
<li><span>allensdk</span></li>
<li><span>biopython</span></li>
<li><span>bokeh</span></li>
<li><span>Dask</span></li>
<li><span>napari</span></li>
<li><span>nilearni</span></li>
<li><span>neuron</span></li>
<li><span>pandas</span></li>
<li><span>pytorch</span></li>
<li><span>scikit-image</span></li>
<li><span>scikit-learn</span></li>
<li><span>starfish</span></li>
<li><span>Theano</span></li>
</ul>
<p><span>To see a full list of packages of packages, run the command in terminal</span></p>
<pre><code>pip list
</code></pre>
<div class="alert alert-info">
<p><img class="emoji" alt=":bulb:"
src="https://cdn.jsdelivr.net/npm/@hackmd/[email protected]/dist/images/basic/bulb.png"><span> Nothing prevents you from downloading and installing your own Anaconda/Miniconda distro in your home directory. However, user supported is limited if you choose to do so.</span>
</p>
<p><span>For more info, click </span><a href="https://docs.anaconda.com/anaconda/install/linux/"
target="_blank"
rel="noopener"><span>here</span></a><span>.</span></p>
</div>
<h4 id="Using-Jupyter-Notebooks-on-the-large-memory-nodes"
data-id="Using-Jupyter-Notebooks-on-the-large-memory-nodes"><a class="anchor hidden-xs"
href="#Using-Jupyter-Notebooks-on-the-large-memory-nodes"
title="Using-Jupyter-Notebooks-on-the-large-memory-nodes"><span
class="octicon octicon-link"></span></a><span>Using Jupyter Notebooks on the large memory nodes</span>
</h4>
<p><span>This document explains how to run a Jupyter notebook on BIL using a Jupyter client on the workshop VM.</span>
</p>
<p>
<span>Follow the steps below to run a Jupyter notebook on using a Jupyter client on your local machine.</span>
</p>
<ol>
<li><span>Login to the workshop VM using </span><code>x2go</code><span>.</span></li>
<li><span>Load an anaconda module to put the latest version of anaconda and Jupyter in your path.</span>
</li>
</ol>
<pre><code>module load anaconda3
</code></pre>
<ol start="3">
<li><span>Get a BIL compute node allocated for your use. Get a BIL compute node allocated for you by using the </span><code>interact</code><span> command. For example,</span>
</li>
</ol>
<pre><code>interact -n 10 --mem=64Gb
A command prompt will appear when your session begins
"Ctrl+d" or "exit" will end your session
</code></pre>
<ol start="5">
<li><span>Find the hostname of the node you are running on</span><br>
<span>You will need the hostname when you are mapping a port on your local machine to the port on BIL compute node. Find the hostname of the node you are on from the prompt, or type the hostname command.</span>
</li>
</ol>
<pre><code>04:37:12 icaoberg@l001 ~ → hostname
l001.pvt.bil.psc.edu
</code></pre>
<ol start="6">
<li><span>Start a Jupyter notebook and find the port number and token</span><br>
<span>Start a Jupyter notebook. From the output of that command, find the port that you are running on and your token. Pay attention to the port number you are given. You will need it to make the connection between the compute node and the workshop VM.</span>
</li>
</ol>
<p><span>The port number Jupyter uses on the compute node can be different each time a notebook is started. Jupyter will attempt first to use port 8888, but if it is taken - by a different Jupyter user for example - it increases the port number by one and tries again, and repeats this until it finds a free port. The one it settles on is the one it will report.</span>
</p>
<pre><code>jupyter notebook --no-browser --ip=0.0.0.0
[W 2022-03-22 16:45:13.993 LabApp] 'ip' has moved from NotebookApp to ServerApp. This config will be passed to ServerApp. Be sure to update your config before our next release.
[W 2022-03-22 16:45:13.994 LabApp] 'ip' has moved from NotebookApp to ServerApp. This config will be passed to ServerApp. Be sure to update your config before our next release.
[W 2022-03-22 16:45:13.994 LabApp] 'ip' has moved from NotebookApp to ServerApp. This config will be passed to ServerApp. Be sure to update your config before our next release.
[I 2022-03-22 16:45:14.013 LabApp] JupyterLab extension loaded from /bil/packages/anaconda3/4.11.0/lib/python3.9/site-packages/jupyterlab
[I 2022-03-22 16:45:14.013 LabApp] JupyterLab application directory is /bil/packages/anaconda3/4.11.0/share/jupyter/lab
[I 16:45:14.024 NotebookApp] Serving notebooks from local directory: /bil/users/icaoberg
[I 16:45:14.024 NotebookApp] Jupyter Notebook 6.4.5 is running at:
[I 16:45:14.025 NotebookApp] http://l001.pvt.bil.psc.edu:8888/?token=6dd14be951e5717631f9646d292a7dae06c8173c1d850c1b
[I 16:45:14.025 NotebookApp] or http://127.0.0.1:8888/?token=6dd14be951e5717631f9646d292a7dae06c8173c1d850c1b
[I 16:45:14.025 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 16:45:14.039 NotebookApp]
To access the notebook, open this file in a browser:
file:///bil/users/icaoberg/.local/share/jupyter/runtime/nbserver-1022410-open.html
Or copy and paste one of these URLs:
http://l001.pvt.bil.psc.edu:8888/?token=6dd14be951e5717631f9646d292a7dae06c8173c1d850c1b
or http://127.0.0.1:8888/?token=6dd14be951e5717631f9646d292a7dae06c8173c1d850c1b
</code></pre>
<ol start="7">
<li><span>Map a port on your local machine to the port Jupyter is using on the BIL compute node. Open another terminal to map the port 8888 in the workshop VM machine to the port you are using (8888 in this example) on the compute node. This is a bit of the chicken-and-the-egg situation: if you knew what node and what port you would end up on, you could have done the mapping on the first connection. But there is no way to know that a-priori.</span>
</li>
</ol>
<p><span>In the new terminal type</span></p>
<pre><code>ssh -L <local-port>:<compute-host-name>:<compute-node-port> workshop.bil.psc.edu -l <username>
</code></pre>
<p><span>You must use the correct compute node name and port that you have been allocated. In this case, because you were connected to port 8888 on compute node r001, that command would look like</span>
</p>
<pre><code>ssh -L 8888:l001.pvt.bil.psc.edu:8888 workshop.bil.psc.edu -l icaoberg
</code></pre>
<p>
<span>Here the localhost port is </span><code>8888</code><span>. After the first </span><code>:</code><span> comes the long name of the compute node, a colon, and the port where Jupyter is running. Here, that string is </span><code>l001.pvt.bil.psc.edu:8888</code><span>.</span>
</p>
<ol start="8">
<li><span>Open a browser window to connect to the Jupyter server. On the workshop VM machine, open a browser and point it to </span><code>http://localhost:8888</code><span>.</span>
</li>
</ol>
<p><img src="https://i.imgur.com/TRFxBOz.png" alt="" loading="lazy"></p>
<p><span>You will be prompted to enter a token to make the connection. Use the token given to when you started the Jupyter server on the BIL compute node (step 6 above).</span>
</p>
<p><img src="https://i.imgur.com/FD6AdCo.png" alt="" loading="lazy"></p>
<ol start="9">
<li><span>When you are done, close your interactive session on BIL.</span></li>
</ol>
<h3 id="Using-Matlab" data-id="Using-Matlab" style=""><a class="anchor hidden-xs" href="#Using-Matlab"
title="Using-Matlab"><span
class="octicon octicon-link"></span></a><span>Using Matlab</span></h3>
<p><span>If you wish to use Matlab, then please request permission to use it first by filling this </span><a
href="https://www.psc.edu/resources/software/matlab/permission-form/" target="_blank"
rel="noopener"><span>form</span></a><span>.</span></p>
<p><span>After getting access you can use it with</span></p>
<pre><code>module load matlab/2021a
matlab -nosplash
</code></pre>
<p><img src="https://i.imgur.com/PYjCKva.png" alt="" loading="lazy"></p>
<h3 id="Using-ITK-SNAP" data-id="Using-ITK-SNAP" style=""><a class="anchor hidden-xs" href="#Using-ITK-SNAP"
title="Using-ITK-SNAP"><span
class="octicon octicon-link"></span></a><span>Using ITK-SNAP</span></h3>
<p><span>ITK-SNAP is a software application used to segment structures in 3D medical images.</span></p>
<pre><code>module load itksnap/3.8.0
itksnap
</code></pre>
<p><img src="https://i.imgur.com/WLRsLk4.png" alt="" loading="lazy"></p>
<h3 id="Installing-and-using-SimpleITK" data-id="Installing-and-using-SimpleITK" style=""><a
class="anchor hidden-xs" href="#Installing-and-using-SimpleITK"
title="Installing-and-using-SimpleITK"><span class="octicon octicon-link"></span></a><span>Installing and using SimpleITK</span>
</h3><img src="https://itk.org/Wiki/images/9/95/SimpleITK-SquareTransparentLogo.png" width="25%">
<pre><code>module load anaconda3/4.11.0
python -m venv .
source ./bin/activate
pip install numpy scipy SimpleITK
</code></pre>
<p><span>For example, to load an image as a numpy array</span></p>
<pre><code>import SimpleITK as sitk
import numpy as np
file = '/bil/data/hackathon/2022_GYBS/data/subject/201606_red_mm_RSA.nii.gz'
image = sitk.ReadImage(file)
arr = sitk.GetArrayFromImage(image)
</code></pre>
<p><span>If you are using iPython you can confirm this</span></p>
<pre><code>In [2]: whos
Variable Type Data/Info
-------------------------------
arr ndarray 1090x942x997: 1023699660 elems, type `uint8`, 1023699660 bytes (976.2760734558105 Mb)
file str /bil/data/hackathon/2022_<...>/201606_red_mm_RSA.nii.gz
image Image Image (0x55faa4652f50)\n <...> Capacity: 1023699660\n
np module <module 'numpy' from '/bi<...>kages/numpy/__init__.py'>
sitk module <module 'SimpleITK' from <...>s/SimpleITK/__init__.py'>
</code></pre>
<div class="alert alert-info">
<p><img class="emoji" alt=":bulb:"
src="https://cdn.jsdelivr.net/npm/@hackmd/[email protected]/dist/images/basic/bulb.png"><span> If you are working in virtual environment you might also want to install other useful libraries like</span>
</p>
<pre><code>pip install matplotlib scipy pandas
</code></pre>
</div>
<h3 id="Installing-ITK" data-id="Installing-ITK" style=""><a class="anchor hidden-xs" href="#Installing-ITK"
title="Installing-ITK"><span
class="octicon octicon-link"></span></a><span>Installing ITK</span></h3><img
src="https://itk.org/wp-content/uploads/2019/10/ITK_Logo_Large-300x143.png">
<pre><code>module load anaconda3/4.11.0
pip install --user itk
</code></pre>
<p><span>or</span></p>
<pre><code>module load anaconda3/4.11.0
python -m venv .
source ./bin/activate
pip install itk
</code></pre>
<p><span>For a quick guide to ITK please visit </span><a
href="https://itkpythonpackage.readthedocs.io/en/master/Quick_start_guide.html" target="_blank"
rel="noopener"><span>here</span></a><span>.</span></p>
<p><span>For example, to read an image</span></p>
<pre><code>import itk
import numpy as np
# Read input image
file = '/bil/data/hackathon/2022_GYBS/data/subject/201606_red_mm_RSA.nii.gz'
itk_image = itk.imread(file)
# View only of itk.Image, pixel data is not copied
np_view = itk.array_view_from_image(itk_image)
</code></pre>
<p><span>If you are using iPython you can confirm this</span></p>
<pre><code>Variable Type Data/Info
---------------------------------------
file str /bil/data/hackathon/2022_<...>/201606_red_mm_RSA.nii.gz
itk LazyITKModule <module 'itk' from '/bil/<...>ackages/itk/__init__.py'>
itk_image itkImageUC3 Image (0x5653b5da85f0)\n <...> Capacity: 1023699660\n
np module <module 'numpy' from '/bi<...>kages/numpy/__init__.py'>
np_view NDArrayITKBase [[[0 0 0 ... 0 0 0]\n [0<...>0]\n [0 0 0 ... 0 0 0]]]
</code></pre>
<div class="alert alert-info">
<p><img class="emoji" alt=":bulb:"
src="https://cdn.jsdelivr.net/npm/@hackmd/[email protected]/dist/images/basic/bulb.png"><span> If you are working in virtual environment you might also want to install other useful libraries like</span>
</p>
<pre><code>pip install matplotlib scipy pandas
</code></pre>
</div>
<h3 id="Installing-nibabel" data-id="Installing-nibabel" style=""><a class="anchor hidden-xs"
href="#Installing-nibabel"
title="Installing-nibabel"><span
class="octicon octicon-link"></span></a><span>Installing nibabel</span></h3>
<p><img src="https://nipy.org/nibabel/_static/nibabel-logo.svg"><br><br>
<span>Read/write access to some common neuroimaging file formats.</span></p>
<pre><code>module load anaconda3/4.11.0
pip install --user nibabel
</code></pre>
<p><span>or</span></p>
<pre><code>module load anaconda3/4.11.0
python -m venv .
source ./bin/activate
pip install nibabel
</code></pre>
<h3 id="Installing-cwltool" data-id="Installing-cwltool" style=""><a class="anchor hidden-xs"
href="#Installing-cwltool"
title="Installing-cwltool"><span
class="octicon octicon-link"></span></a><span>Installing cwltool</span></h3><img
src="https://repository-images.githubusercontent.com/43816051/ba006580-04d7-11eb-9bab-c6463ba5022b"
width="30%">
<pre><code>module load anaconda3/4.11.0
pip install --user cwltool cwlref-runner
</code></pre>
<p><span>or</span></p>
<pre><code>module load anaconda3/4.11.0
python -m venv .
source ./bin/activate
pip install cwltool cwlref-runner
</code></pre>
<h3 id="Installing-spyder" data-id="Installing-spyder" style=""><a class="anchor hidden-xs"
href="#Installing-spyder"
title="Installing-spyder"><span
class="octicon octicon-link"></span></a><span>Installing </span><code>spyder</code></h3>
<p><span>Spyder is a free and open source scientific environment written in Python, for Python, and designed by and for scientists, engineers and data analysts.</span>
</p>
<pre><code>export QT_XCB_GL_INTEGRATION=none
module load anaconda3/4.11.0
python3 -m venv .
source ./bin/activate
pip install spyder
spyder
</code></pre>
<p><img src="https://i.imgur.com/mc56akf.png" alt="" loading="lazy"></p>
<h2 id="Exercises" data-id="Exercises" style=""><a class="anchor hidden-xs" href="#Exercises"
title="Exercises"><span
class="octicon octicon-link"></span></a><span>Exercises</span></h2>
<h3 id="Exercise-0-Submit-a-job-using-OpenOnDemand" data-id="Exercise-0-Submit-a-job-using-OpenOnDemand"
style=""><a class="anchor hidden-xs" href="#Exercise-0-Submit-a-job-using-OpenOnDemand"
title="Exercise-0-Submit-a-job-using-OpenOnDemand"><span
class="octicon octicon-link"></span></a><span>Exercise 0. Submit a job using OpenOnDemand</span>
</h3>
<p><img src="https://i.imgur.com/2XE2OGe.png" alt="" loading="lazy"></p>
<p><img src="https://i.imgur.com/EdCHSoS.png" alt="" loading="lazy"></p>
<h3 id="Exercise-0-Hello-World-on-Jupyter-Lab" data-id="Exercise-0-Hello-World-on-Jupyter-Lab" style=""><a
class="anchor hidden-xs" href="#Exercise-0-Hello-World-on-Jupyter-Lab"
title="Exercise-0-Hello-World-on-Jupyter-Lab"><span class="octicon octicon-link"></span></a><span>Exercise 0. </span><code>Hello,
World!</code><span> on Jupyter Lab</span></h3>
<h3 id="Exercise-1-Load-and-combine-images-in-Fiji" data-id="Exercise-1-Load-and-combine-images-in-Fiji"
style=""><a class="anchor hidden-xs" href="#Exercise-1-Load-and-combine-images-in-Fiji"
title="Exercise-1-Load-and-combine-images-in-Fiji"><span
class="octicon octicon-link"></span></a><span>Exercise 1. Load and combine images in Fiji</span>
</h3><h4 id="Loading-the-proper-module1" data-id="Loading-the-proper-module"><a class="anchor hidden-xs"
href="#Loading-the-proper-module1"
title="Loading-the-proper-module1"><span
class="octicon octicon-link"></span></a><span>Loading the proper module</span></h4>
<p><span>Click the black terminal icon in the top left corner of your screen</span><br>
<img src="https://i.imgur.com/sIGIxvP.png" alt="" loading="lazy"></p>
<p><span>When the terminal opens, type the following commands to load Fiji into your workspace.</span></p>
<pre><code>module load fiji
fiji
</code></pre>
<p><span>The first time running these commands, the system will install Fiji in your home directory.</span>
</p>
<div class="alert alert-info">
<p><img class="emoji" alt=":bulb:"
src="https://cdn.jsdelivr.net/npm/@hackmd/[email protected]/dist/images/basic/bulb.png"><span> If the font size in your terminal is too small, you can press CTRL and + to increase the font size.</span>
</p>
<p><img src="https://i.imgur.com/Ch82FcC.png" alt="" loading="lazy"></p>
</div>
<p><span>After running the commands above, a toolbar should appear in your screen, similar to the picture below</span>
</p>
<p><img src="https://i.imgur.com/My93FBc.png" alt="" loading="lazy"></p><h4 id="Update-Fiji-optional"
data-id="Update-Fiji-optional">
<a class="anchor hidden-xs" href="#Update-Fiji-optional" title="Update-Fiji-optional"><span
class="octicon octicon-link"></span></a><span>Update Fiji (optional)</span></h4>
<p><img src="https://i.imgur.com/FAnec4v.png" alt="" loading="lazy"></p>
<p><span>and then update the plugins</span></p>
<p><img src="https://i.imgur.com/xgYtNKm.png" alt="" loading="lazy"></p><h4 id="Loading-the-first-channel"
data-id="Loading-the-first-channel">
<a class="anchor hidden-xs" href="#Loading-the-first-channel" title="Loading-the-first-channel"><span
class="octicon octicon-link"></span></a><span>Loading the first channel</span></h4>
<p><span>On the "(Fiji Is Just) ImageJ" window select menu</span></p>
<pre><code>[PLUGINS]->[BIOFORMATS][BIOFORMATS-IMPORTER]
</code></pre>
<p><img src="https://i.imgur.com/JjAc2xQ.png" alt="" loading="lazy"></p>
<p><span>Click on FILE SYSTEM in the PLACES sidebar and navigate to</span></p>
<pre><code>/bil/workshops/2021/data_submission/data/fiji/stitchedImage_ch1
</code></pre>
<p><img src="https://i.imgur.com/5VA6Yvh.png" alt="" loading="lazy"></p>
<p><span>then click on</span></p>
<pre><code>StitchedImage_Z001_L001.jp2
</code></pre>
<p><img src="https://i.imgur.com/QbkvvMg.png" alt="" loading="lazy"></p>
<p><span>On the "Bio-Formats Input Options" popup select</span></p>
<p><img src="https://i.imgur.com/5aHcipk.png" alt="" loading="lazy"></p>
<p><span>-View Stack with Hyperstack</span><br>
<span>-Group files with similar names</span><br>
<span>-Color mode: Custom</span><br>
<span>-Click [OK]</span></p>
<p><span>On the "Bio-Formats File Stitching" popup select</span></p>
<p><img src="https://i.imgur.com/JNNfG3e.png" alt="" loading="lazy"></p>
<p><span>-Axis 1 number of images enter 5</span><br>
<span>-Axis 1 axis first image enter 1</span><br>
<span>-Axis 1 axis increment enter 54</span><br>
<span>-Click [OK]</span></p>
<p><span>On the "Bio-Formats Series Options" popup select</span></p>
<p><img src="https://i.imgur.com/pVvsSnM.png" alt="" loading="lazy"></p>
<p><span>-Series 1 (8557x11377)</span><br>
<span>-Click [OK]</span></p>
<p><span>On the "Bio-Formats Custom Colorization" popup select</span></p>
<p><img src="https://i.imgur.com/2Z9qVJ3.png" alt="" loading="lazy"></p>
<p><span>-Series 0 channel 0 Red 255</span><br>
<span>-Click [OK]</span></p><h4 id="Loading-the-second-channel" data-id="Loading-the-second-channel"><a
class="anchor hidden-xs" href="#Loading-the-second-channel" title="Loading-the-second-channel"><span
class="octicon octicon-link"></span></a><span>Loading the second channel</span></h4>
<p><span>We will follow a similar procedure as the first channel</span></p>
<p><span>On the "(Fiji Is Just) ImageJ" window select</span></p>
<pre><code>[PLUGINS]->[BIOFORMATS][BIOFORMATS-IMPORTER]
</code></pre>
<p><img src="https://i.imgur.com/0SERFvc.png" alt="" loading="lazy"></p>
<p><span>Click on FILE SYSTEM in the PLACES sidebar and navigate to</span></p>
<pre><code>/bil/workshops/2021/data_submission/data/fiji/stitchedImage_ch2
</code></pre>
<p><span>then click on</span></p>
<pre><code>StitchedImage_Z001_L001.jp2