eamag/protocols-with-steps huggingface dataset:
TITLE: Whole Gut Transit Time, Fecal Water Content, and Fecal Output
AUTHORS: Jessica Griffiths, Bryan Yoo, Sarkis Mazmanian

[DESCRIPTION]
This protocol was used in "Peripheral Neuronal Activation Shapes the Microbiome and Alters Gut Physiology"

[STEPS]
SECTION: Experiment Preparation
1. 6% (w/v) carmine red (Sigma-Aldrich, St. Louis, MO) with 0.5% methylcellulose (Sigma-Aldrich)
 was dissolved and autoclaved prior to use.
SECTION: Experiment
2. Mice were administered C21 (3 mg/kg) intraperitoneally, and subsequently orally
gavaged with 150 µL of carmine red solution.
SECTION: Experiment
3. Following gavage, mice were single-housed with no bedding for the duration of the experiment, and
animals were not fasted beforehand.
SECTION: Experiment
4. Over the 5 hours following gavage, the time of expulsion was recorded for each fecal
pellet, and each pellet was collected in pre-weighed, 1.5 mL microcentrifuge
tube.
SECTION: Experiment
5. Each pellet collected was checked for the presence of carmine red, and the time of
initial carmine red pellet expulsion was recorded as GI transit time.
SECTION: Sample Processing
6. The mass of collected fecal pellets was determined, and pellets were left to dry in
an 80 ºC oven for 2 days before weighing the desiccated pellets and calculating
the pellets’ initial water content. 
SECTION: Data Analysis
7. Fecal output rate for each mouse was calculated as the total number of pellets
expelled during the 5 hour time course post-C21 administration divided by the
time the last fecal pellet was expelled.
TITLE: Automation Protocol for Plasmid DNA Extraction from E. coli
AUTHORS: Nina Alperovich, Jane Romantseva,  Olga Vasilyeva, David Ross

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Here, we describe a protocol for automated extraction of plasmid DNA from 24 E. coli cultures. The protocol uses an automated liquid handler and a positive pressure filter press. It is based on the QIAprep Spin Miniprep Kit (Qiagen, 27106).</div><div class = "text-block"><span>This protocol requires an automated liquid handler (Hamilton Robotics, STAR) with both 8-channel and 96-channel pipetting heads and positive pressure filter press (Hamilton, MPE2). It also requires a centrifuge with a 96-well plate rotor capable of at least 3878 </span><span style = "font-style:italic;">g.</span></div></div>

[STEPS]
?. Pellet cell cultures in 96-well deep-well plate by centrifugation at 3878 g (4500 rpm) for 10 minutes at 23 °C.
?. Remove supernatant from the wells containing each cell pellet.
?. Resuspend each cell pellet in in 200 µL of Resuspension Buffer; mix 10x by repeated aspiration and dispense.
?. Transfer resuspended cell samples to a new 96-well plate (Abgene, AB-1127) located on an automated microplate shaker.
?. Add 250 µL Lysate Buffer to each sample and mix by shaking the plate at 90 rpm for 2 minutes.
?. Add 350 µL cold (4 °C) Neutralization Buffer (Qiagen, 19064) to each sample and mix by shaking at 90 rpm for 2 minutes.
?. Using wide bore tips (3.2 mm tip diameter), gently mixed the lysate samples by 3 repeated cycles of aspiration and dispensing, then transfer samples to a 96-well filter plate (Agilent, 201702-100) and allowed to settle in the filter plate for 2 minutes.
?. Use the filter press to push the lysate solutions through the filter plate into a new 96-well deep well plate (Eppendorf, 951033588) at 20 psi for 180 s followed by 65 psi for 30 s.
?. Transfer the cleared lysate solutions to a 96-well glass fiber binding plate (Nunc, 278010) and use the filter press to push the solutions through the binding plate at 40 psi for 60 s.
?. Add 900 µL Binding Buffer (Qiagen, 19066) to each well and use the filter press to push buffer through the binding plate at 40 psi for 60 s.
?. Add 900 µL Wash Buffer to each well and use the filter press to push buffer through the binding plate at 40 psi for 60 s.
?. Use the filter press to dry the binding plate by applying 65 psi for 7 minutes.
?. Add 100 µL nuclease-free water (Thermo Scientific, AM9938) warmed to 60 °C to each well; wait for 5 minutes.
?. Elute DNA from binding plate into a 96-well low-binding elution plate (Eppendorf, 30603303) using the filter press at 65 psi for 7 minutes.
TITLE: Immunoblot analysis for immunodetection of HIV proteins.
AUTHORS: Angel  Justiz-Vaillant

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Enzyme-Linked Immunosorbent Assay (ELISA) was used for screening while the Western Blot was used for confirmation.</div></div>

[STEPS]
?. Aliquots of 3-5 µl of the serum are applied to the gel and run on a protein electrophoresis (SDS-PAGE).
?. Gels are transferred to nitrocellulose membranes (Immobilon-Nc, pore size 0.45 µm, during 75 min at 40 mAmps using a semi-dry electroblotter, HEP-1 Model, Owl Scientific Inc).
?. The running buffer contains 25mM Tris, 192mM glycine pH 8.3 and 20% methanol.
?. The nitrocellulose membranes are blocked overnight in 10% nonfat skim milk in PBS with 0.05% Tween-20 pH 7.4 and then washed 4 times for 10 minutes with PBS-Tween 20.
?. Peroxidase-labeled anti-HIV conjugate are added and incubated at 4ºC overnight.
?. Membranes are washed as above and then tetra-methyl-benzidine are added and the reaction is stopped with deionised water.
?. A positive test displays two or more HIV proteins.
?. Only patients with positive confirmatory tests are classified as HIV positive.
TITLE: KAPP-Sen TMC: Dissociation of Pancreatic Islets (non-recovered) Protocol
AUTHORS: Juliana Alcoforado Diniz, Paul Robson, Dylan Baker, Jessica Garofalo

[DESCRIPTION]
The dispersed samples were shipped cold from PRODOLABS.
Prior to scRNA-seq, dispersed samples from brain dead donor’s pancreatic acinar
and ducts were dissociated as follows.




[STEPS]
SECTION: Abstract
1. The dispersed samples were shipped cold from PRODOLABS.
Prior to scRNA-seq, dispersed samples from brain dead donor’s pancreatic acinar
and ducts were dissociated as follows.
SECTION: Cell Dissociation with TrypLE
2. NOTE: Before beginning cell dissociation coat all the materials (pipettes, tubes, etc.) with stopping media to prevent sticking. Stopping Media: DMEM + 10% FBS + 1:100 Glutamate.
1. Distribute specimens into 50 ml conical tubes, try to make similar cell concentrations across all tubes. *** Receive acinar in ~300 ml, should distribute into 12 tubes with 25 ml each***
2. Centrifuge acinar samples for 2 min at 230 g and 4C. Leave duct samples to settle without disturbance.
3. Wash samples 3X with 25 ml PBS.
4.  Add 10 ml TrypLE E and incubate at 37C, mixing with a pipette approximately every 5 min.
            i. Acinar: in TrypLE E at 37C for approximately 30 mins.
            ii. Ducts: in TrypLE E at 37C for approximately 15 mins.
5. To stop reaction, add 30 ml per tube of stopping media.
6. Centrifuge acinar and ducts at 1300 rpm, 4C, 2 mins.
7. To stop: add 30 ml per tube of stopping media.
8. Centrifuge acinar and ducts at 1300 rpm, 4C, 2 mins.
9.  Aspirate TrypLE E and wash 1X with stop media. Aspirate then resuspend in stop media to (Acinar) 5 ml or (Ducts) 2 ml.
10. Transfer cell suspension through 70 µm filter then combine to 2 ml (Acinar) and 1ml (Ducts). Filter again through a 40 µm Flowmi.
11. Count cells using AO/PI (acridine orage/propidium iodide) Cell Viability Kit for Luna-FL automated cell counter.
12. Proceed to cell fixation.
SECTION: Fixation of Cells &amp; Nuclei for Chromium Fixed RNA Profiling
3. Cells were fixated prior to scRNAseq according to https://dx.doi.org/10.17504/protocols.io.[...] /v1
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
In this protocol, we perform a metabolic profiling of metagenomic datasets using <a href="http://huttenhower.sph.harvard.edu/humann" target="_blank">HUMAnN</a> applied to the 20 samples taxonomically profiled in the other protocols contained in this collection.<br /><br />Once the metabolic profile has been generated, the following protocols can be performed:<br />
<ul>
<li>MetaPhlAn output merge and visualizations</li>
<li>GraPhlAn visualization of single and multiple samples</li>
<li>Taxonomic biomarker discovery with LEfSe</li>
</ul>

[BEFORE_START]
REQUIREMENTS: <a href="http://huttenhower.sph.harvard.edu/humann" target="_blank">HUMAnN</a>, <a href="http://www.scons.org/" target="_blank">scons</a>, the KEGG protein DB. HUMAnN can be obtained using <a href="http://mercurial.selenic.com/" target="_blank">Mercurial</a>: <code>hg clone ssh://hg@bitbucket.org/chuttenh/humann</code> or using the direct links to the <a href="https://bitbucket.org/chuttenh/humann/get/default.zip" target="_blank">zip</a>, <a href="https://bitbucket.org/chuttenh/humann/get/default.gz" target="_blank">gz</a>, or <a href="https://bitbucket.org/chuttenh/humann/get/default.bz2" target="_blank">bz2</a> archives.

[GUIDELINES]
<p>Metabolic profiles of the 20 HMP samples with HUMAnN can be generated with the following steps:</p>
<ul>
<li>Perform a translated search (using <a href="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/" target="_blank">blastx</a> or <a href="http://www.drive5.com/usearch/" target="_blank">usearch</a>) against the KEGG DB. Since HUMAnN's development KEGG has become commercial, we are currently developing support for other data sources.</li>
<li>Place the translated BLAST results using KEGG gene identifiers in the <code>input</code> directory (optionally can be gzipped or bzipped, several other formats can be enabled editing the settings in the <code>SConstruct</code> file).</li>
<li>Run the <code>scons</code> command, optionally parallelizing multiple analyses using the <code>-j</code> flag. Results will be placed in the "output" directory.</li>
</ul>
<br />We provide the HUMAnN output for users who want to perform the downstream analysis pipeline but avoid the computational intensive steps above. The 20 samples profiled with HUMAnN are available <a href="https://bitbucket.org/nsegata/metaphlan/wiki/humann_profiling.tar.bz2" target="_blank">here</a>.<br /><br />Using HUMAnN output, you can perform the metabolic counterpart of the taxonomic pipeline presented in this tutorial. With a table of metabolomic abundances, the previous protocols can be performed with little to no modification. We report below the first command to obtain the merged table of metabolic abundances.<br /><br />
<pre>$ mkdir output
$ utils/merge_metaphlan_tables.py humann_profiling/*.txt &gt; output/merged_humann_abundance_table.txt</pre>

[STEPS]
?. 
?. 
?. 
?. 
?.
TITLE: No Title
AUTHORS: 

[GUIDELINES]
<p><strong>Materials and Buffers</strong></p>
<p>1. Chamber slides or cover slips</p>
<p>2. Fixation solution: 4% Paraformaldehyde, in PBS</p>
<p>3. Permeablization solution: 0.5% Triton X-100 in PBS</p>
<p>4. Antibody dilution solution: 5%FBS in PBS</p>

[STEPS]
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?.
TITLE: qPercerus
AUTHORS: Robert Loewe, Benedikt Kirchner

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Protocol for qPercerus SARS-CoV-2 Test (attached document is giving more details). </div><div class = "text-block">Final product will be a commercial kit that is consisting of four components (lysis buffer, primer/probe mix identification, primer/probe mix confirmation, qPCR master mix). The initial test for SARS-CoV-2 is the identification assay (FAM assay for S gene with HEX assay as internal control) for patient screening. The confirmation assay (FAM assay for Orf3a with HEX assay as internal control) is used to re-evaluate the results.</div></div>

[STEPS]
?. Add  to reaction tube
[Lysis Buffer]
?. Add Nasopharyngeal or Throat Swab to Lysis Buffer and swivel for   to lysate and inactivate virus. Remove and discard the Swab afterwards.
If Nasopharyngeal and Throat Swab are available from the same patient, the sensitivity can be increased by using both in one qPercerus reaction.
?. Briefly vortex and incubate at  for
0 Room temperature
Sample is stable in Lysis Buffer for up to    at   allowing for storage and transport.
?. Mix RT-qPCR Master Mix for first Identification Assay with 10% surplus and distribute on suitable qPCR microtiter plate:  per reaction per reaction
[ID Primer/Probe Mix]
[Master Mix]
?. Add virus lysate to each well on qPCR microtiter plate:
[Virus Lysate]
?. Briefly spin down qPCR microtiter plate
Centrifuge: 1000 34, 30 s
?. Run One-Step RT-qPCR with the following temperature protocol:For 45 cycles:FAM channel detects SARS-CoV-2 related fluorescenceHEX channel detects human Internal Control related fluorescence
50 °C
[reverse transcription]
95 °C
[RT Inactivation/ Polymerase activation]
95 °C
60 °C
[aquiring on FAM and HEX]
?. Evaluate Cqs of HEX channel for swab validity:Cq of HEX Cq of HEX >30    inconclusive -> perform Confirmation Assay for validationEvaluate Cqs of FAM channel for SARS-CoV-2 presence: Cq of FAM 40 > Cq of FAM >35       inconclusive -> perform Confirmation Assay for validationCq of FAM >40 or NA    negative for SARS-CoV-2
If national testing regulations demand validation of positive SARS-CoV-2 presence on an independent target sequence, perform Confirmation Assay for Cq of FAM
?. Mix RT-qPCR Master Mix for first Confirmation Assay with 10% surplus and distribute on suitable qPCR microtiter plate:  per reaction per reaction
[CONF Primer/Probe Mix]
[Master Mix]
?. Add virus lysate to each well on qPCR microtiter plate:
[Virus Lysate]
?. Briefly spin down qPCR microtiter plate
Centrifuge: 1000 34, 30 s
?. Run One-Step RT-qPCR with the following temperature protocol:For 45 cycles:FAM channel detects SARS-CoV-2 related fluorescenceCy5 channel detects human Internal Control related fluorescence
50 °C
[reverse transcription]
95 °C
[RT Inactivation/ Polymerase activation]
95 °C
60 °C
[aquiring on FAM and HEX]
?. Evaluate Cqs of HEX channel for swab validity:Cq of HEX Cq of HEX >30    sample invalid, repeat sampling ofEvaluate Cqs of HEX channel for SARS-CoV-2 presence: Cq of FAM Cq of FAM >40 or NA    negative for SARS-CoV-2
TITLE: No Title
AUTHORS: 

[STEPS]
SECTION: Laminating sample film
?. 
SECTION: Laminating sample film
?. 
SECTION: Collecting bacteria and counting colonies
?. 
SECTION: Collecting bacteria and counting colonies
?. 
SECTION: Collecting bacteria and counting colonies
?. 
SECTION: The rules of counting
?. 
SECTION: The rules of counting
?. 
SECTION: The rules of counting
?. 
SECTION: The rules of counting
?.
TITLE: Freezing Adherent Cell Lines
AUTHORS: Carolina Lopez

[DESCRIPTION]
This protocol describes how to freeze Adherent cells. Examples of these cells are: A549 cells, LLCMK2 cells, and MDCK cells.

[STEPS]
SECTION: Freezing Adherent cells
1. 
*Try to freeze cells at the lowest passage possible and confirm the cells are negative for mycoplasma before freezing. 

Wash flask 2x with sterile 1X PBS.
Add 2mL of trypsin/T75. Incubate at 37ºC for 2-3 mins or until cells are detached from the flask.
Add 8mL of cell culture media and pipette up and down. Transfer all the media to a 15mL tube. 
Centrifuge at 1200 rpm for 5 min. 
Discard supernatant and resuspend cell pellet in 1mL of cell culture media. Add 9mL of media and pipette up and down to homogenize. 
Count the cells. You will need your cell concentration/# for step 6.
Spin the tube containing the cells in media again at 1200 rpm for 5 min. 
Meanwhile, prepare the freezing medium (see materials for recipe). Prepare the amount of freezing medium needed to dilute the cell pellet so that you have a final concentration of 1*106 cells/mL. 
Discard the supernatant and resuspend the pellet in 1mL of freezing medium. Add the remaining volume of the freezing medium. Make sure you homogenize the solution well. 
Add 1mL of freezing medium containing 1*106 cells/mL to cryotubes (caps screw from the outside). Label all the tubes with the following information:
Cell Name
Generation/Passage
Date
Name
Cell concentration (if there is space)
11. Transfer the cells to a Mr. Frosty Freezing container containing isopropanol and then transfer the container to the -80ºC for 1 day. After 1 day, transfer the tubes to the liquid nitrogen. You can keep some vials in the -80ºC for a couple of months, however, the -80ºC is not for long-term storage.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Optimised VENTANA BenchMark ULTRA protocol for PD-L1 assay using the concentrate 22C3 antibody.</p>
<p>For the purpose of protocol development 95% of clinical specimens consisted of surgical resection specimens and the remaining 5% were bronchial biopsies and transbronchial mediastinal lymph node biopsies.</p>

[GUIDELINES]
<p>Scoring and Interpretation of the staining:<br />The Tumor Proportion Score (TPS) of the PDL-1 expression for the specimen</p>
<p> </p>
<p>The TPS is the percentage of viable cells showing partial or complete staining (≥ 1%) relative to all viable tumor cells positive or negative present in the sample. TPS should be evaluated on at least 100 viable cells in the specimen.<br />Specimens are interpreted as having:<br />- No PDL-1 expression: TPS &lt; 1%<br />- Any PDL-1 expression: TPS ≥ 1%<br />Specimens expressing PDL-1 can be divided into PDL-1 expressing: TPS 1% to 49% and high PD-L1 expressing TPS≥ 50%.<br />For more information regarding the Interpretation of the scoring please refer to PDL-1 IHC 22C3 PharmDx-Interpretation manual: http://www.dako.com/us/29109_pd-l1-ihc-22c3-interpretation-manual.pdf </p>

[STEPS]
?. 
?. 
?. 
?. 
?.
TITLE: Nanostring GeoMx Digital Spatial Profiler (DSP) protocols -- University of Minnesota TMCs
AUTHORS: Nanostring, Grant Barthel, Laura Niedernhofer, David A Bernlohr

[DESCRIPTION]
Applicable Nanostring GeoMx DSP protocols for University of Minnesota 

[STEPS]
1. GeoMx DSP Manual Slide Preparation User Manual
  

2. Quick Guide: GeoMx Manual Slide Preparation: RNA FFPE
  

3. Quick Guide: GeoMx Semi-Automated Slide Preparation: Protein FFPE
TITLE: Prescription patterns of somatostatin analogues in patients with acromegaly and neuroendocrine tumors
AUTHORS: Jorge        Machado Alba

[DESCRIPTION]
Objective. Acromegaly and neuroendocrine tumors are rare diseases that, under certain conditions, can be treated with somatostatin analogues. The aim was to determine the prescription patterns of somatostatin analogues in a group of patients with acromegaly and neuroendocrine tumors affiliated with the Colombian Health System.
Design. A retrospective study.
Methods: A cohort of patients from a drug dispensing database that collected all prescriptions of long-acting somatostatin analogues (octreotide, lanreotide, pasireotide). Sociodemographic variables, clinical variables (diagnosis and comorbidities) and pharmacological therapy variables (dose, changes, persistence of use, comedications) were considered.
Results: A total of 213 patients were identified, including 139 (65.3%) with acromegaly and 74 (34.7%) with neuroendocrine tumors. There was a predominance of women (58.7%) and a mean age of 59.7 ± 14.5 years. The most commonly used medications were lanreotide autogel (n = 107; 50.2%), octreotide LAR (n = 102; 47.9%) and pasireotide LAR (n = 4; 1.9%). During follow-up, 11.3% of patients experienced modifications of therapy, with a mean duration from the beginning of treatment to the change in medication of 25 ± 15.9 months. A total of 48.9% of the patients with acromegaly and 87.1% of individuals with neuroendocrine tumors received maximum approved doses of the drug.
Conclusions: Patients with acromegaly and neuroendocrine tumors in Colombia are mainly women and are most frequently treated with lanreotide autogel for acromegaly and with octreotide LAR for neuroendocrine tumors. In addition, a high proportion are managed with maximum doses of long-acting somatostatin analogues.

[STEPS]
TITLE: Protocolo de avaliação clínica audiológica para crianças com microcefalia
AUTHORS: Klinger Vagner Teixeira da Costa, Luis Pedro Coelho

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Trata-se de uma ficha de anamneses direcionada para avaliação audiológica em crianças com a síndrome congênita do vírus da Zica.</div></div>

[STEPS]
TITLE: Protein extraction of zebrafish and fathead minnow embryos
AUTHORS: Laura Langan

[DESCRIPTION]
This protocol describes an optimized protein extraction method for proteomic analyses for zebrafish and fathead minnow embryo's aged ~96 hpf/dpf (species dependent), and wouldn't have been possible without the following papers

References: 

Masuda, T., Tomita, M., Ishihama, Y., 2008. Phase Transfer Surfactant-Aided Trypsin Digestion for Membrane Proteome Analysis. J. Proteome Res. 7, 731–740. https://doi.org/10.1021/pr700658q

Lin Y, Lin H, Liu Z, Wang K, Yan Y. Improvement of a sample preparation method assisted by sodium deoxycholate for mass-spectrometry-based shotgun membrane proteomics. J Sep Sci. 2014; 37(22): 3321-9. doi: 10.1002/jssc.201400569

Rappsilber, J., Ishihama, Y., Mann, M., 2003. Stop And Go Extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal. Chem. 75, 663–670. https://doi.org/10.1021/ac026117i

Wiśniewski, J.R., 2016. Quantitative Evaluation of Filter Aided Sample Preparation (FASP) and Multienzyme Digestion FASP Protocols. Analytical Chemistry 88, 5438–5443. https://doi.org/10.1021/acs.analchem.6b00859

Wiśniewski, J.R., Zougman, A., Nagaraj, N., Mann, M., 2009. Universal sample preparation method for proteome analysis. Nat. Methods 6, 359–362. https://doi.org/10.1038/nmeth.1322

[BEFORE_START]
Before starting
Prepare stock solutions
 Samples can be lysed and quantified in advance and stored at -20/-80   C, therefore sample preparation and peptide digestion are separated into two categories. If samples are prepared in advance, then only PBS wash solution, lysis buffer and 10 % SDS stock need to be made in advance. 
Defrost and store samples on ice
Pre-heat thermo-shaker (95 °C)


 


Stock solutions

PBS wash solution
1 tablet/100 mL of water

Lysis buffer
0.1 M Tris-HCL (pH 7.8)
0.05 M DTT
cOmplete Ultra tablets (Protease inhibitor cocktail) [1 tablet/10 mL buffer]

10 % SDS stock solution (w/v) [HPLC water]

UA buffer
2 M Urea (pH 8.5;  0.1 M Tris-HCL)

Digestion buffer (DB)
ABC buffer (50 mM)

DTT buffer 
45   1 M stock to 955   HPLC water

IAA stock (1M)
189 mg/1 mL ABC buffer

Sodium deoxycholate (SDC), 10 % (w/v)


Elution buffer
70 % NaCL [1 M] + 30 % methanol
ABC buffer (sodium bicarbonate)

5 % TFA (v/v)


Equipment
Micro-centrifuge
Tissue homogenizer (e.g. Scilogex D160 homogenizer + saw tooth probe)
Sonicating probe (Misonix sonicator; ultrasonic liquid processor with micro-tip)
ThermoMixer C eppendorf + smartblock and/or heating block
Speedvac


[GUIDELINES]
Wear appropriate safety clothing (lab coat, safety goggles, gloves, mask) at all times. Wear mask especially when handling DTT, SDS and SDC. 

Pelleted SDS is safer and more convenient to handle than SDS powder. Please also refer to the respective MSDS sheets.

[STEPS]
TITLE: CODA: 3D tissue reconstruction pipeline | HuBMAP | JHU-TMC
AUTHORS: Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Sashank Reddy, Denis Wirtz

[DESCRIPTION]
CODA pipeline with 6 parts

[STEPS]
SECTION: Setting up CODA environment and preparing sample dataset
1. dx.doi.org/10.17504/protocols.io.q26g71rpkgwz/v1
SECTION: Calculate registration on low-resolution tissue images
2. dx.doi.org/10.17504/protocols.io.kxygxym3dl8j/v1
SECTION: Deep learning multi-labelling of tissue structures using training on manual annotations
3. dx.doi.org/10.17504/protocols.io.81wgbz1x3gpk/v1
SECTION: Register the deep learning labelled images and Construct 3D tissue matrix
4. dx.doi.org/10.17504/protocols.io.yxmvme7eog3p/v1
SECTION: Nuclear coordinate generation
5. dx.doi.org/10.17504/protocols.io.dm6gpz8z8lzp/v1
SECTION: Register the nuclear coordinates and Construct 3D cell matrix
6. dx.doi.org/10.17504/protocols.io.n2bvjnrnxgk5/v1