diff --git a/ioSPI/datasets.py b/ioSPI/datasets.py
index edd502c..af662b4 100644
--- a/ioSPI/datasets.py
+++ b/ioSPI/datasets.py
@@ -28,6 +28,8 @@ class Project:
     """
 
     def __init__(self, username: str, token: str, project_id: str = "7g42j") -> None:
+        self.username = username
+        self.token = token
         self.project_id = project_id
 
         config_path = os.path.join(".osfcli.config")
@@ -80,7 +82,7 @@ def upload(self, remote_path, local_path):
             E.g. 4v6x_randomrot_copy6_defocus3.0_yes_noise.txt
         """
         print(f"Uploading {local_path} to {remote_path}...")
-        os.system(f"osf upload {local_path} {remote_path} ")
+        os.system(f"osf upload {local_path} {remote_path}")
         print("Done!")
 
 
diff --git a/notebooks/download_and_upload_with_osf.ipynb b/notebooks/download_and_upload_with_osf.ipynb
index 904b920..3a8d957 100644
--- a/notebooks/download_and_upload_with_osf.ipynb
+++ b/notebooks/download_and_upload_with_osf.ipynb
@@ -1,2390 +1,2559 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "id": "a820b6f9",
-   "metadata": {},
-   "source": [
-    "# Download and Upload with OSF\n",
-    "\n",
-    "This tutorial shows how to download and upload cryo-EM datasets using the `datasets` module from `ioSPI`, that interact with the [Open Science Foundation (OSF)](https://osf.io/) framework.\n",
-    "\n",
-    "OSF is an initiative that aims to increase the openness, reproducibility and integrity of scientific research. Among other functionalities, it is possible to upload scientific data which can be accessed by an Application Programming Interface (API). \n",
-    "\n",
-    "``ioSPI`` offers functionalities that allow uploading and accessing cryo-EM data using:\n",
-    "- either, in order to get started: using the class `Project` that leverages the package `osfclient`\n",
-    "- or, if the user requires finer control: using the class `OSFUpload` which follows `OSF APIv2`. \n",
-    "\n",
-    "This tutorial introduces both options."
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "e60fbfce",
-   "metadata": {},
-   "source": [
-    "# Set-up"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "869c66c3",
-   "metadata": {},
-   "source": [
-    "First, you will need to get setup with osf.\n",
-    "\n",
-    "- Create an account on https://osf.io/ and save the email address you use.\n",
-    "- On this account, create a personal token in [Settings](https://osf.io/settings/tokens) and save it.\n",
-    "\n",
-    "The email address and the token will be needed to connect to different OSF projects.\n",
-    "\n",
-    "We import the `datasets` module from `ioSPI`:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "id": "e74dd634",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from ioSPI.ioSPI import datasets"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "cfc8e678",
-   "metadata": {},
-   "source": [
-    "# Getting Started"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "c74b27f6",
-   "metadata": {},
-   "source": [
-    "## Configure your credentials to access the OSF Project"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "2e4d58a3",
-   "metadata": {},
-   "source": [
-    "Find the OSF project from which you wish to download your data. \n",
-    "\n",
-    "In this tutorial, we use a project called \"cryoEM simulated\" which contains simulated images from the 80s human ribosome. This project is on osf at the url: \"https://osf.io/7g42j/\".\n",
-    "\n",
-    "- Save the ID of the project of interest, which appears in the project's url.\n",
-    "\n",
-    "In our case, the project ID is `7g42k`.\n",
-    "\n",
-    "- Create an object from the class `Project` using:\n",
-    "  - your credentials from the set up: email address and token,\n",
-    "  - the project ID that you just saved."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "id": "febfdedd",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "OSF config written to .osfcli.config!\n"
-     ]
-    }
-   ],
-   "source": [
-    "cryoem_simulated_project = datasets.Project(\n",
-    "    username=\"ninamio78@gmail.com\", \n",
-    "    token=\"HBGGBOJcLYQfadEKIOyXJiLTum3ydXK4nGP3KmbkYUeBuYkZma9LPBSYennQn92gjP2NHn\",\n",
-    "    project_id=\"7g42j\")"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "633b4dd8",
-   "metadata": {},
-   "source": [
-    "You have successfully set up the configuration of the OSF project!\n",
-    "\n",
-    "## List Files on the OSF Project\n",
-    "\n",
-    "Now you can list the files available on this OSF project. Note that this code can take a few minutes to run."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "id": "f4f5b054",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Listing files from OSF project: 7g42j...\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy7_defocus1.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy1_defocus1.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy4_defocus2.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy8_defocus0.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus0.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus3.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy1_defocus2.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy7_defocus3.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus2.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy4_defocus2.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy4_defocus2.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus0.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus2.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy8_defocus1.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy5_defocus2.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy5_defocus2.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy8_defocus2.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy5_defocus1.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy3_defocus2.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus1.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy9_defocus0.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy3_defocus3.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy3_defocus2.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy5_defocus1.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy3_defocus2.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy9_defocus3.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy4_defocus1.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy6_defocus2.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy4_defocus3.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy2_defocus1.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy1_defocus1.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy6_defocus0.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy2_defocus2.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus1.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy5_defocus2.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy8_defocus2.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy2_defocus0.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy2_defocus3.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy3_defocus1.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy2_defocus2.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy5_defocus1.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy2_defocus1.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy3_defocus3.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy3_defocus1.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy8_defocus3.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy1_defocus0.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy7_defocus2.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus1.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy1_defocus1.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy5_defocus0.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy6_defocus1.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy9_defocus0.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy9_defocus2.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy2_defocus1.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy1_defocus3.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy7_defocus1.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy4_defocus0.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy6_defocus3.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy2_defocus1.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy2_defocus3.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy7_defocus2.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy9_defocus1.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus1.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy3_defocus1.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy7_defocus2.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus3.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy8_defocus0.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy3_defocus0.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy8_defocus2.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy8_defocus2.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy2_defocus0.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus2.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy6_defocus2.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy8_defocus1.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy5_defocus3.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy4_defocus1.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy5_defocus2.0_yes_noise.txt\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy4_defocus2.0_no_noise.mrc\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy7_defocus1.5_yes_noise.log\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy6_defocus2.5_no_noise.inp\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy8_defocus1.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy9_defocus2.0_yes_noise.log\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy1_defocus1.0_no_noise.log\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy6_defocus3.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy0_defocus2.0_no_noise.log\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy4_defocus0.5_yes_noise.txt\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy1_defocus1.5_yes_noise.inp\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy1_defocus0.5_yes_noise.txt\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy0_defocus1.5_no_noise.log\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy3_defocus2.5_yes_noise.log\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy6_defocus3.0_yes_noise.log\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy8_defocus0.5_no_noise.log\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy2_defocus2.0_yes_noise.mrc\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy8_defocus1.0_yes_noise.inp\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy4_defocus3.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy9_defocus3.0_no_noise.log\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy7_defocus2.5_yes_noise.txt\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy3_defocus1.5_yes_noise.inp\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy0_defocus1.5_yes_noise.log\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy9_defocus3.0_yes_noise.log\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy2_defocus2.0_yes_noise.inp\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy5_defocus0.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy4_defocus1.0_no_noise.mrc\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy5_defocus2.5_yes_noise.inp\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy7_defocus2.0_yes_noise.mrc\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy6_defocus1.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy9_defocus1.0_yes_noise.mrc\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy8_defocus3.0_yes_noise.txt\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy4_defocus0.5_no_noise.mrc\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy4_defocus1.5_no_noise.txt\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy7_defocus1.5_yes_noise.inp\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy7_defocus1.5_no_noise.mrc\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy9_defocus2.5_yes_noise.mrc\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy4_defocus1.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy1_defocus1.5_yes_noise.log\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy4_defocus3.0_no_noise.mrc\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy4_defocus0.5_no_noise.inp\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy2_defocus1.0_no_noise.txt\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy3_defocus3.0_yes_noise.mrc\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy8_defocus1.5_yes_noise.log\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy1_defocus3.0_yes_noise.log\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy6_defocus1.0_no_noise.inp\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy3_defocus3.0_yes_noise.inp\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy7_defocus3.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy6_defocus2.0_no_noise.mrc\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy3_defocus2.0_no_noise.txt\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy5_defocus1.0_no_noise.txt\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy7_defocus1.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy4_defocus2.0_yes_noise.inp\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy5_defocus3.0_no_noise.inp\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy9_defocus1.0_yes_noise.txt\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy2_defocus0.5_no_noise.inp\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy8_defocus1.5_no_noise.log\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy8_defocus1.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy2_defocus0.5_yes_noise.log\n",
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-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy6_defocus1.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy8_defocus2.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy7_defocus2.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy9_defocus3.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy5_defocus1.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy7_defocus2.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy8_defocus3.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy7_defocus1.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy3_defocus2.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy8_defocus1.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy4_defocus0.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy2_defocus0.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy6_defocus1.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy3_defocus2.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy4_defocus1.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy9_defocus1.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy2_defocus1.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy9_defocus1.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy1_defocus2.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy2_defocus2.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy1_defocus3.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy1_defocus1.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy5_defocus2.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy4_defocus1.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy1_defocus3.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy3_defocus2.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy0_defocus0.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy7_defocus2.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy2_defocus2.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy3_defocus2.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy6_defocus2.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy5_defocus3.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy4_defocus1.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy7_defocus3.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy5_defocus2.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy0_defocus1.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy9_defocus1.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy5_defocus0.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy8_defocus3.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy7_defocus1.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy3_defocus2.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy8_defocus1.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy0_defocus2.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy4_defocus2.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy1_defocus0.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy1_defocus2.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy0_defocus2.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy4_defocus2.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy0_defocus2.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy2_defocus1.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy2_defocus2.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy6_defocus2.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy2_defocus3.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy2_defocus1.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy1_defocus3.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy7_defocus0.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy1_defocus1.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy0_defocus0.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy6_defocus1.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy1_defocus1.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy7_defocus1.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy4_defocus0.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy0_defocus1.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy6_defocus1.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy8_defocus3.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy5_defocus1.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy2_defocus3.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy6_defocus3.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy9_defocus1.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy6_defocus1.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy7_defocus1.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy0_defocus3.0_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy5_defocus1.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy2_defocus2.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy5_defocus2.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy9_defocus0.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy3_defocus0.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy4_defocus1.5_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy9_defocus0.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy3_defocus3.0_yes_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy7_defocus0.5_no_noise.h5\n",
-      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy6_defocus1.5_no_noise.h5\n"
-     ]
-    }
-   ],
-   "source": [
-    "cryoem_simulated_project.ls()"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "274a0e01",
-   "metadata": {},
-   "source": [
-    "We observe that this project contains many files, organized in different folders.\n",
-    "\n",
-    " ## Download Files from the OSF Project\n",
-    "\n",
-    "We can download one of these files, e.g. choosing from the above list the following txt file:\n",
-    "\n",
-    "- `osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy0_defocus3.0_yes_noise.txt`.\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 5,
-   "id": "6f5270f4",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Downloading osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy0_defocus3.0_yes_noise.txt to 4v6x_randomrot_copy0_defocus3.0_yes_noise.txt...\n",
-      "Done!\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "\r",
-      "  0%|          | 0.00/4.22k [00:00<?, ?bytes/s]\r",
-      "100%|██████████| 4.22k/4.22k [00:00<00:00, 9.90Mbytes/s]\n"
-     ]
-    }
-   ],
-   "source": [
-    "cryoem_simulated_project.download(\n",
-    "    remote_path=\"osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy0_defocus3.0_yes_noise.txt\", \n",
-    "    local_path=\"4v6x_randomrot_copy0_defocus3.0_yes_noise.txt\")"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "5956e4e3",
-   "metadata": {},
-   "source": [
-    "## Upload Files to an OSF Project"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "c7846400",
-   "metadata": {},
-   "source": [
-    "Importantly, OSF will not let you upload data to any folder: authorization is requested.\n",
-    "\n",
-    "To test this functionality, you can create a new project through osf.io (https://osf.io/myprojects/) by clicking: `Create project`.\n",
-    "\n",
-    "This will create a new project page, as the one we are using here.\n",
-    "- Save the project ID of the project you just created!\n",
-    "\n",
-    "You should then create a new `my_project` object of the class `datasets.Project` with the new project ID.\n",
-    "\n",
-    "For the purpose of this tutorial, however, we will stay with our original project cryoEM simulated and use our object `cryoem_simulated_project`.\n",
-    "\n",
-    "We re-upload the file that we just downloaded, renaming it by adding a `new_version` prefix to its name."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 6,
-   "id": "74c6125e",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Uploading 4v6x_randomrot_copy0_defocus3.0_yes_noise.txt to osfstorage/randomrot1D_nodisorder/new_version_4v6x_randomrot_copy0_defocus3.0_yes_noise.txt...\n",
-      "Done!\n"
-     ]
-    }
-   ],
-   "source": [
-    "cryoem_simulated_project.upload(\n",
-    "    remote_path=\"osfstorage/randomrot1D_nodisorder/new_version_4v6x_randomrot_copy0_defocus3.0_yes_noise.txt\", \n",
-    "    local_path=\"4v6x_randomrot_copy0_defocus3.0_yes_noise.txt\")"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "9b03f00a",
-   "metadata": {},
-   "source": [
-    "Congratulations! You have successfully uploaded and downloaded data from OSF."
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.4"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "a820b6f9",
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
+   "source": [
+    "# Download and Upload with OSF\n",
+    "\n",
+    "This tutorial shows how to download and upload cryo-EM datasets using the `datasets` module from `ioSPI`, that interact with the [Open Science Foundation (OSF)](https://osf.io/) framework.\n",
+    "\n",
+    "OSF is an initiative that aims to increase the openness, reproducibility and integrity of scientific research. Among other functionalities, it is possible to upload scientific data which can be accessed by an Application Programming Interface (API). \n",
+    "\n",
+    "``ioSPI`` offers functionalities that allow uploading and accessing cryo-EM data using:\n",
+    "- either, in order to get started: using the class `Project` that leverages the package `osfclient`\n",
+    "- or, if the user requires finer control: using the class `OSFUpload` which follows `OSF APIv2`. \n",
+    "\n",
+    "This tutorial introduces both options."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "e60fbfce",
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
+   "source": [
+    "# Set-up"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "869c66c3",
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
+   "source": [
+    "First, you will need to get setup with osf.\n",
+    "\n",
+    "- Create an account on https://osf.io/ and save the email address you use.\n",
+    "- On this account, create a personal token in [Settings](https://osf.io/settings/tokens) and save it.\n",
+    "\n",
+    "The email address and the token will be needed to connect to different OSF projects.\n",
+    "\n",
+    "We import the `datasets` module from `ioSPI`:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "e74dd634",
+   "metadata": {
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "# Temp for non-conda. Remove later.\n",
+    "import sys\n",
+    "sys.path.append('../../')\n",
+    "\n",
+    "\n",
+    "from ioSPI.ioSPI import datasets"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "cfc8e678",
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
+   "source": [
+    "# Getting Started"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c74b27f6",
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
+   "source": [
+    "## Configure your credentials to access the OSF Project"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2e4d58a3",
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
+   "source": [
+    "Find the OSF project from which you wish to download your data. \n",
+    "\n",
+    "In this tutorial, we use a project called \"cryoEM simulated\" which contains simulated images from the 80s human ribosome. This project is on osf at the url: \"https://osf.io/7g42j/\".\n",
+    "\n",
+    "- Save the ID of the project of interest, which appears in the project's url.\n",
+    "\n",
+    "In our case, the project ID is `7g42j`.\n",
+    "\n",
+    "- Create an object from the class `Project` using:\n",
+    "  - your credentials from the set up: email address and token,\n",
+    "  - the project ID that you just saved."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "febfdedd",
+   "metadata": {
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OSF config written to .osfcli.config!\n"
+     ]
+    }
+   ],
+   "source": [
+    "cryoem_simulated_project = datasets.Project(\n",
+    "    username=\"ninamio78@gmail.com\", \n",
+    "    token=\"HBGGBOJcLYQfadEKIOyXJiLTum3ydXK4nGP3KmbkYUeBuYkZma9LPBSYennQn92gjP2NHn\",\n",
+    "    project_id=\"7g42j\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "633b4dd8",
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
+   "source": [
+    "You have successfully set up the configuration of the OSF project!\n",
+    "\n",
+    "## List Files on the OSF Project\n",
+    "\n",
+    "Now you can list the files available on this OSF project. Note that this code can take a few minutes to run."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "f4f5b054",
+   "metadata": {
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Listing files from OSF project: 7g42j...\n",
+      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy7_defocus1.0_no_noise.h5\n",
+      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy1_defocus1.5_yes_noise.h5\n",
+      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy4_defocus2.0_no_noise.h5\n",
+      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy8_defocus0.5_no_noise.h5\n",
+      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus0.5_no_noise.h5\n",
+      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus3.0_no_noise.h5\n",
+      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy1_defocus2.5_no_noise.h5\n",
+      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy7_defocus3.0_no_noise.h5\n",
+      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus2.0_yes_noise.h5\n",
+      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy4_defocus2.0_yes_noise.h5\n",
+      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy4_defocus2.5_no_noise.h5\n",
+      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus0.5_yes_noise.h5\n",
+      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy0_defocus2.5_yes_noise.h5\n",
+      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy8_defocus1.0_no_noise.h5\n",
+      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy5_defocus2.5_no_noise.h5\n",
+      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy5_defocus2.5_yes_noise.h5\n",
+      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy8_defocus2.0_yes_noise.h5\n",
+      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy5_defocus1.0_yes_noise.h5\n",
+      "osfstorage/randomrot1D_nodisorder/final/4v6x_randomrot_copy3_defocus2.5_no_noise.h5\n",
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+      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy5_defocus1.0_yes_noise.h5\n",
+      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy2_defocus3.0_no_noise.h5\n",
+      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy6_defocus3.0_yes_noise.h5\n",
+      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy9_defocus1.0_yes_noise.h5\n",
+      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy6_defocus1.0_no_noise.h5\n",
+      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy7_defocus1.0_yes_noise.h5\n",
+      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy0_defocus3.0_no_noise.h5\n",
+      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy5_defocus1.5_yes_noise.h5\n",
+      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy2_defocus2.5_yes_noise.h5\n",
+      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy5_defocus2.5_no_noise.h5\n",
+      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy9_defocus0.5_yes_noise.h5\n",
+      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy3_defocus0.5_no_noise.h5\n",
+      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy4_defocus1.5_yes_noise.h5\n",
+      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy9_defocus0.5_no_noise.h5\n",
+      "osfstorage/randomrot1D_multiPDB/3ja1_randomrot_copy3_defocus3.0_yes_noise.h5\n",
+      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy7_defocus0.5_no_noise.h5\n",
+      "osfstorage/randomrot1D_multiPDB/3j9z_randomrot_copy6_defocus1.5_no_noise.h5\n"
+     ]
+    }
+   ],
+   "source": [
+    "cryoem_simulated_project.ls()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "274a0e01",
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
+   "source": [
+    "We observe that this project contains many files, organized in different folders.\n",
+    "\n",
+    " ## Download Files from the OSF Project\n",
+    "\n",
+    "We can download one of these files, e.g. choosing from the above list the following txt file:\n",
+    "\n",
+    "- `osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy0_defocus3.0_yes_noise.txt`.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "6f5270f4",
+   "metadata": {
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Downloading osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy0_defocus3.0_yes_noise.txt to 4v6x_randomrot_copy0_defocus3.0_yes_noise.txt...\n",
+      "Done!\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "100%|██████████| 4.22k/4.22k [00:00<00:00, 19.1Mbytes/s]\n"
+     ]
+    }
+   ],
+   "source": [
+    "cryoem_simulated_project.download(\n",
+    "    remote_path=\"osfstorage/randomrot1D_nodisorder/4v6x_randomrot_copy0_defocus3.0_yes_noise.txt\", \n",
+    "    local_path=\"4v6x_randomrot_copy0_defocus3.0_yes_noise.txt\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5956e4e3",
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
+   "source": [
+    "## Upload Files to an OSF Project"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c7846400",
+   "metadata": {
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
+   "source": [
+    "Importantly, OSF will not let you upload data to any folder: authorization is requested.\n",
+    "\n",
+    "To test this functionality, you can create a new project through osf.io (https://osf.io/myprojects/) by clicking: `Create project`.\n",
+    "\n",
+    "This will create a new project page, as the one we are using here.\n",
+    "- Save the project ID of the project you just created!\n",
+    "\n",
+    "You should then create a new `my_project` object of the class `datasets.Project` with the new project ID.\n",
+    "\n",
+    "For the purpose of this tutorial, however, we will stay with our original project cryoEM simulated and use our object `cryoem_simulated_project`.\n",
+    "\n",
+    "We re-upload the file that we just downloaded, renaming it by adding a `new_version` prefix to its name. We will first create a child node inside the parent node which corresponds to our root directory. Then, we will upload the file to ths child node.\n",
+    "\n",
+    "To do this, let's create an instance of ``OSFUpload`` class which takes care of uploading data to ``osf.io``. Provide the personal token and project ID."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "74c6125e",
+   "metadata": {
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "{'Authorization': 'Bearer HBGGBOJcLYQfadEKIOyXJiLTum3ydXK4nGP3KmbkYUeBuYkZma9LPBSYennQn92gjP2NHn'}\n"
+     ]
+    }
+   ],
+   "source": [
+    "osf = datasets.OSFUpload(token=cryoem_simulated_project.token, data_node_guid=cryoem_simulated_project.project_id)\n",
+    "print(osf.headers)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "Now we create a child node inside the parent node, for representing the dataset with 80s ribosome data. We will use the pdb id as the name for this new node, and the function will return its ID. Since the child is also a node, it can be accessed separately from the parent node."
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "64cx2\n"
+     ]
+    }
+   ],
+   "source": [
+    "pdb_id = '4v6x'\n",
+    "child_guid = osf.write_child_node(parent_guid=cryoem_simulated_project.project_id, title= pdb_id)\n",
+    "print(child_guid)"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "Now, we finally upload the files related to the 80s ribosome to the child node using ``write_files`` function. Note the ``file_paths`` must be a list, thus ``[]`` is needed around the filepaths."
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
+   "outputs": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Uploaded 4v6x_randomrot_copy0_defocus3.0_yes_noise.txt \n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": "True"
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "osf.write_files(child_guid, [\"4v6x_randomrot_copy0_defocus3.0_yes_noise.txt\"])"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "We can now check if it was uploaded correctly using the function `read_structure_guid` which will return an ID corresponding to the pdb id passed as a parameter."
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "outputs": [
+    {
+     "data": {
+      "text/plain": "'ezh4k'"
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "osf.read_structure_guid(pdb_id)"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "Congratulations! You have successfully downloaded and uploaded data from/to OSF."
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   }
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "name": "venv_iospi",
+   "language": "python",
+   "display_name": "venv_iospi"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
\ No newline at end of file
diff --git a/notebooks/tutorial.ipynb b/notebooks/tutorial.ipynb
index 75ef485..1249e4e 100644
--- a/notebooks/tutorial.ipynb
+++ b/notebooks/tutorial.ipynb
@@ -1,431 +1,416 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# ioSPI\n",
-    "In this tutorial we will explain the basic pipeline of ``ioSPI``. Library which provides functionalities to work with cryo-EM data."
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Particle Metadata\n",
-    "\n",
-    "In the first part of the tutorial we show how to create a `.star` file using the module `particle_metadata`. This module basically format and write particle metadata as `.star` files, following RELION conventions."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import os\n",
-    "import sys\n",
-    "import warnings\n",
-    "\n",
-    "sys.path.append(os.path.dirname(os.getcwd()))\n",
-    "warnings.filterwarnings('ignore')"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "In order to create the `.star` file is necessary to provide information about the experiment, such as the image pixel size and image center shift. This information is passed in the form of a list and a `Config` object."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from ioSPI.ioSPI import particle_metadata\n",
-    "\n",
-    "class Config:\n",
-    "    \"\"\"Class to instantiate the config object.\"\"\"\n",
-    "    def __init__(self, ctf, shift):\n",
-    "        self.ctf = ctf\n",
-    "        self.shift = shift"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "data_list = [[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14]]\n",
-    "config = Config(ctf=True, shift=True)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "The names of the metadata for the star file (in RELION convention) can be accessed using the function `get_starfile_metadata_names` passing a `Config` object."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 5,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "['__rlnImageName', '__rlnAngleRot', '__rlnAngleTilt', '__rlnAnglePsi', '__rlnOriginX', '__rlnOriginY', '__rlnDefocusU', '__rlnDefocusV', '__rlnDefocusAngle', '__rlnVoltage', '__rlnImagePixelSize', '__rlnSphericalAberration', '__rlnAmplitudeContrast', '__rlnCtfBfactor']\n"
-     ]
-    }
-   ],
-   "source": [
-    "variable_names = particle_metadata.get_starfile_metadata_names(config)\n",
-    "print(variable_names)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Using the list of values and the `Config` object it is possible to format the `.star` file that will be later saved with the `format_metadata_for_writing_cryoem_convention` function, which creates a dataframe with the data."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 6,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<div>\n",
-       "<style scoped>\n",
-       "    .dataframe tbody tr th:only-of-type {\n",
-       "        vertical-align: middle;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe tbody tr th {\n",
-       "        vertical-align: top;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe thead th {\n",
-       "        text-align: right;\n",
-       "    }\n",
-       "</style>\n",
-       "<table border=\"1\" class=\"dataframe\">\n",
-       "  <thead>\n",
-       "    <tr style=\"text-align: right;\">\n",
-       "      <th></th>\n",
-       "      <th>__rlnImageName</th>\n",
-       "      <th>__rlnAngleRot</th>\n",
-       "      <th>__rlnAngleTilt</th>\n",
-       "      <th>__rlnAnglePsi</th>\n",
-       "      <th>__rlnOriginX</th>\n",
-       "      <th>__rlnOriginY</th>\n",
-       "      <th>__rlnDefocusU</th>\n",
-       "      <th>__rlnDefocusV</th>\n",
-       "      <th>__rlnDefocusAngle</th>\n",
-       "      <th>__rlnVoltage</th>\n",
-       "      <th>__rlnImagePixelSize</th>\n",
-       "      <th>__rlnSphericalAberration</th>\n",
-       "      <th>__rlnAmplitudeContrast</th>\n",
-       "      <th>__rlnCtfBfactor</th>\n",
-       "    </tr>\n",
-       "  </thead>\n",
-       "  <tbody>\n",
-       "    <tr>\n",
-       "      <th>0</th>\n",
-       "      <td>1</td>\n",
-       "      <td>2</td>\n",
-       "      <td>3</td>\n",
-       "      <td>4</td>\n",
-       "      <td>5</td>\n",
-       "      <td>6</td>\n",
-       "      <td>7</td>\n",
-       "      <td>8</td>\n",
-       "      <td>9</td>\n",
-       "      <td>10</td>\n",
-       "      <td>11</td>\n",
-       "      <td>12</td>\n",
-       "      <td>13</td>\n",
-       "      <td>14</td>\n",
-       "    </tr>\n",
-       "  </tbody>\n",
-       "</table>\n",
-       "</div>"
-      ],
-      "text/plain": [
-       "   __rlnImageName  __rlnAngleRot  __rlnAngleTilt  __rlnAnglePsi  __rlnOriginX  \\\n",
-       "0               1              2               3              4             5   \n",
-       "\n",
-       "   __rlnOriginY  __rlnDefocusU  __rlnDefocusV  __rlnDefocusAngle  \\\n",
-       "0             6              7              8                  9   \n",
-       "\n",
-       "   __rlnVoltage  __rlnImagePixelSize  __rlnSphericalAberration  \\\n",
-       "0            10                   11                        12   \n",
-       "\n",
-       "   __rlnAmplitudeContrast  __rlnCtfBfactor  \n",
-       "0                      13               14  "
-      ]
-     },
-     "execution_count": 6,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "metadata_df = particle_metadata.format_metadata_for_writing_cryoem_convention(data_list=data_list, config=config)\n",
-    "metadata_df"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "After formatting the data we can use the function `write_metadata_to_starfile` providing the metadata, the path and name of the star file. "
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 7,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "metadata_path = os.path.join(os.getcwd(), \"data\")\n",
-    "filename = \"metadata.star\"\n",
-    "particle_metadata.write_metadata_to_starfile(path=metadata_path, metadata=metadata_df, filename=filename)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Finally, we check whether a `.star` file with the name `metadata.star` was created or not, using the function `check_star` function which will raise an exception if the file is not found."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 8,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "particle_metadata.check_star_file(os.path.join(metadata_path, filename))"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "The file was successfully created as shown by printing its content."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 9,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "# Created by the starfile Python package (version 0.4.11) at 17:35:08 on 27/04/2022\n",
-      "\n",
-      "data_\n",
-      "\n",
-      "loop_\n",
-      "___rlnImageName #1\n",
-      "___rlnAngleRot #2\n",
-      "___rlnAngleTilt #3\n",
-      "___rlnAnglePsi #4\n",
-      "___rlnOriginX #5\n",
-      "___rlnOriginY #6\n",
-      "___rlnDefocusU #7\n",
-      "___rlnDefocusV #8\n",
-      "___rlnDefocusAngle #9\n",
-      "___rlnVoltage #10\n",
-      "___rlnImagePixelSize #11\n",
-      "___rlnSphericalAberration #12\n",
-      "___rlnAmplitudeContrast #13\n",
-      "___rlnCtfBfactor #14\n",
-      "1\t2\t3\t4\t5\t6\t7\t8\t9\t10\t11\t12\t13\t14\n",
-      "\n",
-      "\n",
-      "\n"
-     ]
-    }
-   ],
-   "source": [
-    "with open(os.path.join(metadata_path, filename)) as star_file:\n",
-    "    print(star_file.read())\n",
-    "    star_file.close()"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Datasets\n",
-    "\n",
-    "In the second part of the tutorial we will show how to manage cryo-EM datasets using the `datasets` module from `ioSPI`. This module uses the Open Science Foundation (OSF) framework, which is an initiative that aims to increase the openness, reproducibility and integrity of scientific research. Among other functionalities, it is possible to upload scientific data which can be accessed by an Application Programming Interface (API). ``ioSPI`` offers functionalities that allow uploading and accessing cryo-EM data using the OSF APIv2. This notebook is by no means a tutorial for the OSF API, but we will introduce some basic concepts used here. For more information you can access <https://developer.osf.io/>. The two main components from the OSF that we use here are:\n",
-    "\n",
-    "* GUID: Every file, project, and component on the OSF gets a Globally Unique ID (GUID). The GUID is the five characters after the <https://osf.io/> in the web address. For instance, we provide cryo-EM Datasets with GUID 24htr. There you will find cryo-EM datasets for different proteins.\n",
-    "* Nodes: On OSF files, projects, and components are called nodes, they can be either public or private and it is where the data is contained. For example, <https://osf.io/24htr/> is a node containing cryo-EM data."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 11,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from ioSPI.ioSPI import datasets"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Before following this tutorial you will have to create your own node for upload cryo-EM data and set an access token. The access token is responsible to manage which actions can be performed by the user who possesses the token. After this step it is possible to instantiate an `OSFUpload` object, to access this OSF node using the OSF API by informing the GUID of the node and the access token. "
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 14,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\n"
-     ]
-    }
-   ],
-   "source": [
-    "token = 's9XHmPaLzRoJnNFSLngb2pH6KPtmCOxEgdJitRiQuRROq7omjX8SKyBIgfZYTiC1X0154o'\n",
-    "\n",
-    "guid = '8e5j9'\n",
-    "\n",
-    "osf = datasets.OSFUpload(token = token, data_node_guid= guid)\n",
-    "print(osf.headers)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Now we will create a child node inside the parent node, for representing the dataset with 80s ribosome data. We will use the pdb id as the name for this new node, and the function will return its GUID. Since the child is also a node, it can accessed separately from the parent node."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 15,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "8yg32\n"
-     ]
-    }
-   ],
-   "source": [
-    "pdb_id = '4v6x'\n",
-    "child_guid = osf.write_child_node(parent_guid = guid, title = pdb_id)\n",
-    "print(child_guid)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Having created a child node for putting the files related to the 80s ribosome, we can upload files to it by using the function `write_files`."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 16,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Uploaded c:\\Users\\Luis\\Documents\\GitHub\\ioSPI\\notebooks\\4v6x.pdb \n"
-     ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "True"
-      ]
-     },
-     "execution_count": 16,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "#Create a list of the files to be uploaded\n",
-    "file_paths = [os.path.join(os.getcwd(), 'data', pdb_id + '.pdb')]\n",
-    "\n",
-    "#Write files at the child node\n",
-    "osf.write_files(dataset_guid = child_guid, file_paths = file_paths)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "We can now check if it was uploaded correctly by checking if the function `read_structure_guid` will return a GUID corresponding to the pdb id passed as parameter."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 17,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "'8yg32'"
-      ]
-     },
-     "execution_count": 17,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "osf.read_structure_guid(pdb_id)"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.4"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 2
-}
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "source": [
+    "# ioSPI\n",
+    "In this tutorial we will explain the basic pipeline of ``ioSPI``. Library which provides functionalities to work with cryo-EM data."
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## Particle Metadata\n",
+    "\n",
+    "In the first part of the tutorial we show how to create a `.star` file using the module `particle_metadata`. This module basically format and write particle metadata as `.star` files, following RELION conventions."
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import sys\n",
+    "import warnings\n",
+    "\n",
+    "sys.path.append(os.path.dirname(os.getcwd()))\n",
+    "warnings.filterwarnings('ignore')"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "In order to create the `.star` file is necessary to provide information about the experiment, such as the image pixel size and image center shift. This information is passed in the form of a list and a `Config` object."
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "outputs": [],
+   "source": [
+    "from ioSPI.ioSPI import particle_metadata\n",
+    "\n",
+    "class Config:\n",
+    "    \"\"\"Class to instantiate the config object.\"\"\"\n",
+    "    def __init__(self, ctf, shift):\n",
+    "        self.ctf = ctf\n",
+    "        self.shift = shift"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "outputs": [],
+   "source": [
+    "data_list = [[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14]]\n",
+    "config = Config(ctf=True, shift=True)"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "The names of the metadata for the star file (in RELION convention) can be accessed using the function `get_starfile_metadata_names` passing a `Config` object."
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "outputs": [],
+   "source": [
+    "variable_names = particle_metadata.get_starfile_metadata_names(config)\n",
+    "print(variable_names)"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "Using the list of values and the `Config` object it is possible to format the `.star` file that will be later saved with the `format_metadata_for_writing_cryoem_convention` function, which creates a dataframe with the data."
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "outputs": [],
+   "source": [
+    "metadata_df = particle_metadata.format_metadata_for_writing_cryoem_convention(data_list=data_list, config=config)\n",
+    "metadata_df"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "After formatting the data we can use the function `write_metadata_to_starfile` providing the metadata, the path and name of the star file. "
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "outputs": [],
+   "source": [
+    "metadata_path = os.path.join(os.getcwd(), \"data\")\n",
+    "filename = \"metadata.star\"\n",
+    "particle_metadata.write_metadata_to_starfile(path=metadata_path, metadata=metadata_df, filename=filename)"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "Finally, we check whether a `.star` file with the name `metadata.star` was created or not, using the function `check_star` function which will raise an exception if the file is not found."
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "outputs": [],
+   "source": [
+    "particle_metadata.check_star_file(os.path.join(metadata_path, filename))"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "The file was successfully created as shown by printing its content."
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "outputs": [],
+   "source": [
+    "with open(os.path.join(metadata_path, filename)) as star_file:\n",
+    "    print(star_file.read())\n",
+    "    star_file.close()"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "# Datasets\n",
+    "\n",
+    "In the second part of the tutorial we will show how to manage cryo-EM datasets using the `datasets` module from `ioSPI`. This module uses the Open Science Foundation (OSF) framework, which is an initiative that aims to increase the openness, reproducibility and integrity of scientific research. Among other functionalities, it is possible to upload scientific data which can be accessed by an Application Programming Interface (API). ``ioSPI`` offers functionalities that allow uploading and accessing cryo-EM data using the OSF APIv2. This notebook is by no means a tutorial for the OSF API, but we will introduce some basic concepts used here. For more information you can access <https://developer.osf.io/>. The two main components from the OSF that we use here are:\n",
+    "\n",
+    "* GUID: Every file, project, and component on the OSF gets a Globally Unique ID (GUID). The GUID is the five characters after the <https://osf.io/> in the web address. For instance, we provide cryo-EM Datasets with GUID 24htr. There you will find cryo-EM datasets for different proteins.\n",
+    "* Nodes: On OSF files, projects, and components are called nodes, they can be either public or private and it is where the data is contained. For example, <https://osf.io/24htr/> is a node containing cryo-EM data."
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "outputs": [],
+   "source": [
+    "\n",
+    "# Temp for non-conda. Remove later.\n",
+    "import sys\n",
+    "sys.path.append('../../')\n",
+    "\n",
+    "from ioSPI.ioSPI import datasets"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Before following this tutorial you will have to create your own node for upload cryo-EM data and set an access token. The access token is responsible to manage which actions can be performed by the user who possesses the token. After this step it is possible to instantiate an `OSFUpload` object, to access this OSF node using the OSF API by informing the GUID of the node and the access token. "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "HTTPError",
+     "evalue": "401 Client Error: Unauthorized for url: https://api.osf.io/v2/",
+     "output_type": "error",
+     "traceback": [
+      "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
+      "\u001B[0;31mHTTPError\u001B[0m                                 Traceback (most recent call last)",
+      "Input \u001B[0;32mIn [4]\u001B[0m, in \u001B[0;36m<cell line: 5>\u001B[0;34m()\u001B[0m\n\u001B[1;32m      1\u001B[0m token \u001B[38;5;241m=\u001B[39m \u001B[38;5;124m'\u001B[39m\u001B[38;5;124ms9XHmPaLzRoJnNFSLngb2pH6KPtmCOxEgdJitRiQuRROq7omjX8SKyBIgfZYTiC1X0154o\u001B[39m\u001B[38;5;124m'\u001B[39m\n\u001B[1;32m      3\u001B[0m guid \u001B[38;5;241m=\u001B[39m \u001B[38;5;124m'\u001B[39m\u001B[38;5;124m8e5j9\u001B[39m\u001B[38;5;124m'\u001B[39m\n\u001B[0;32m----> 5\u001B[0m osf \u001B[38;5;241m=\u001B[39m \u001B[43mdatasets\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mOSFUpload\u001B[49m\u001B[43m(\u001B[49m\u001B[43mtoken\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43m \u001B[49m\u001B[43mtoken\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mdata_node_guid\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43m \u001B[49m\u001B[43mguid\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m      6\u001B[0m \u001B[38;5;28mprint\u001B[39m(osf\u001B[38;5;241m.\u001B[39mheaders)\n",
+      "File \u001B[0;32m~/ucsb/projects/compSPI/ioSPI/notebooks/../../ioSPI/ioSPI/datasets.py:116\u001B[0m, in \u001B[0;36mOSFUpload.__init__\u001B[0;34m(self, token, data_node_guid)\u001B[0m\n\u001B[1;32m    113\u001B[0m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mheaders \u001B[38;5;241m=\u001B[39m {\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mAuthorization\u001B[39m\u001B[38;5;124m\"\u001B[39m: \u001B[38;5;124mf\u001B[39m\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mBearer \u001B[39m\u001B[38;5;132;01m{\u001B[39;00mtoken\u001B[38;5;132;01m}\u001B[39;00m\u001B[38;5;124m\"\u001B[39m}\n\u001B[1;32m    114\u001B[0m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mbase_url \u001B[38;5;241m=\u001B[39m \u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mhttps://api.osf.io/v2/\u001B[39m\u001B[38;5;124m\"\u001B[39m\n\u001B[0;32m--> 116\u001B[0m \u001B[43mrequests\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mget\u001B[49m\u001B[43m(\u001B[49m\u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mbase_url\u001B[49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mheaders\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mheaders\u001B[49m\u001B[43m)\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mraise_for_status\u001B[49m\u001B[43m(\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m    118\u001B[0m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mdata_node_guid \u001B[38;5;241m=\u001B[39m data_node_guid\n",
+      "File \u001B[0;32m~/ucsb/projects/compSPI/ioSPI/venv_iospi/lib/python3.8/site-packages/requests/models.py:960\u001B[0m, in \u001B[0;36mResponse.raise_for_status\u001B[0;34m(self)\u001B[0m\n\u001B[1;32m    957\u001B[0m     http_error_msg \u001B[38;5;241m=\u001B[39m \u001B[38;5;124mu\u001B[39m\u001B[38;5;124m'\u001B[39m\u001B[38;5;132;01m%s\u001B[39;00m\u001B[38;5;124m Server Error: \u001B[39m\u001B[38;5;132;01m%s\u001B[39;00m\u001B[38;5;124m for url: \u001B[39m\u001B[38;5;132;01m%s\u001B[39;00m\u001B[38;5;124m'\u001B[39m \u001B[38;5;241m%\u001B[39m (\u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mstatus_code, reason, \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39murl)\n\u001B[1;32m    959\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m http_error_msg:\n\u001B[0;32m--> 960\u001B[0m     \u001B[38;5;28;01mraise\u001B[39;00m HTTPError(http_error_msg, response\u001B[38;5;241m=\u001B[39m\u001B[38;5;28mself\u001B[39m)\n",
+      "\u001B[0;31mHTTPError\u001B[0m: 401 Client Error: Unauthorized for url: https://api.osf.io/v2/"
+     ]
+    }
+   ],
+   "source": [
+    "token = 's9XHmPaLzRoJnNFSLngb2pH6KPtmCOxEgdJitRiQuRROq7omjX8SKyBIgfZYTiC1X0154o'\n",
+    "\n",
+    "guid = '8e5j9'\n",
+    "\n",
+    "osf = datasets.OSFUpload(token = token, data_node_guid= guid)\n",
+    "print(osf.headers)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Now we will create a child node inside the parent node, for representing the dataset with 80s ribosome data. We will use the pdb id as the name for this new node, and the function will return its GUID. Since the child is also a node, it can accessed separately from the parent node."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "8yg32\n"
+     ]
+    }
+   ],
+   "source": [
+    "pdb_id = '4v6x'\n",
+    "child_guid = osf.write_child_node(parent_guid = guid, title = pdb_id)\n",
+    "print(child_guid)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Having created a child node for putting the files related to the 80s ribosome, we can upload files to it by using the function `write_files`."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Uploaded c:\\Users\\Luis\\Documents\\GitHub\\ioSPI\\notebooks\\4v6x.pdb \n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "True"
+      ]
+     },
+     "execution_count": 16,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "#Create a list of the files to be uploaded\n",
+    "file_paths = [os.path.join(os.getcwd(), 'data', pdb_id + '.pdb')]\n",
+    "\n",
+    "#Write files at the child node\n",
+    "osf.write_files(dataset_guid = child_guid, file_paths = file_paths)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We can now check if it was uploaded correctly by checking if the function `read_structure_guid` will return a GUID corresponding to the pdb id passed as parameter."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 17,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'8yg32'"
+      ]
+     },
+     "execution_count": 17,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "osf.read_structure_guid(pdb_id)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "name": "venv_iospi",
+   "language": "python",
+   "display_name": "venv_iospi"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
\ No newline at end of file