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Merged
giovannivolpe merged 12 commits into from
Jul 30, 2026
Merged

tutorials/1-getting-started fix colab links and add notebook installations #503

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acbb771
feat: add necessary library installations in every notebook
foca13 Jul 13, 2026
f4c438d
fix: add missing library installation
foca13 Jul 13, 2026
85dabcb
fix: installation line
foca13 Jul 13, 2026
7c8215d
fix: colab links
foca13 Jul 13, 2026
0982cc5
fix: cell outputs
foca13 Jul 13, 2026
226be8f
fix: example notebooks path
foca13 Jul 14, 2026
e730e2c
Merge branch 'develop' into fix-links-dependencies
foca13 Jul 14, 2026
d6aec16
feat: add missing library installation in getting started notebooks
foca13 Jul 14, 2026
bffdbcb
style: library installation
foca13 Jul 14, 2026
105022b
style: inline comments
foca13 Jul 14, 2026
70d4d7e
Merge branch 'develop' into fix-links-dependencies
foca13 Jul 27, 2026
a172adc
Merge branch 'develop' into fix-links-dependencies
foca13 Jul 29, 2026
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16 changes: 13 additions & 3 deletions tutorials/1-getting-started/DTGS101_intro.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -11,13 +11,23 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# !pip install deeptrack # Uncomment if running on Colab/Kaggle."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# !pip install deeplay # Uncomment if needed.\n",
"# !pip install seaborn # Uncomment if needed."
]
},
{
"cell_type": "markdown",
"metadata": {},
Expand Down Expand Up @@ -972,7 +982,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "py_env_book",
"display_name": "deeptrack2",
"language": "python",
"name": "python3"
},
Expand All @@ -986,7 +996,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.15"
"version": "3.13.14"
}
},
"nbformat": 4,
Expand Down
16 changes: 13 additions & 3 deletions tutorials/1-getting-started/DTGS111_datafiles.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -11,13 +11,23 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# !pip install deeptrack # Uncomment if running on Colab/Kaggle."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# !pip install deeplay # Uncomment if needed.\n",
"# !pip install opencv-python # Uncomment if needed."
]
},
{
"cell_type": "markdown",
"metadata": {},
Expand Down Expand Up @@ -659,7 +669,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "py_env_book",
"display_name": "deeptrack2",
"language": "python",
"name": "python3"
},
Expand All @@ -673,7 +683,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.15"
"version": "3.13.14"
}
},
"nbformat": 4,
Expand Down
18 changes: 14 additions & 4 deletions tutorials/1-getting-started/DTGS121_tracking_particle_cnn.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -11,11 +11,21 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# !pip install deeplay deeptrack # Uncomment if running on Colab/Kaggle."
"# !pip install deeptrack # Uncomment if running on Colab/Kaggle."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# !pip install deeplay # Uncomment if needed.\n",
"# !pip install seaborn # Uncomment if needed."
]
},
{
Expand Down Expand Up @@ -821,7 +831,7 @@
"metadata": {
"file_extension": ".py",
"kernelspec": {
"display_name": "py_env_book (3.10.15)",
"display_name": "deeptrack2",
"language": "python",
"name": "python3"
},
Expand All @@ -835,7 +845,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.15"
"version": "3.13.14"
},
"mimetype": "text/x-python",
"name": "python",
Expand Down
19 changes: 14 additions & 5 deletions tutorials/1-getting-started/DTGS126_characterizing_aberrations_cnn.ipynb
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Expand Up @@ -6,16 +6,25 @@
"source": [
"# DTGS126. Characterizing Aberrations with a CNN\n",
"\n",
"<a href=\"https://colab.research.google.com/github/softmatterlab/DeepTrack-2.0/blob/develop/examples/tutorials/1-getting-started/DTSG126_characterizing_aberrations_cnn.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
"<a href=\"https://colab.research.google.com/github/DeepTrackAI/DeepTrack2/blob/develop/tutorials/1-getting-started/DTGS126_characterizing_aberrations_cnn.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
]
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# !pip install deeptrack # Uncomment if running on Colab/Kaggle."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# !pip install deeplay deeptrack # Uncomment if running on Colab/Kaggle."
"# !pip install deeplay # Uncomment if needed."
]
},
{
Expand Down Expand Up @@ -556,7 +565,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "py_env_book (3.10.15)",
"display_name": "deeptrack2",
"language": "python",
"name": "python3"
},
Expand All @@ -570,7 +579,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.15"
"version": "3.13.14"
}
},
"nbformat": 4,
Expand Down
18 changes: 14 additions & 4 deletions tutorials/1-getting-started/DTGS127_characterizing_aberrations_optuna.ipynb
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Expand Up @@ -12,12 +12,22 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 2,
"id": "1d3be940",
"metadata": {},
"outputs": [],
"source": [
"# !pip install deeptrack optuna # Uncomment if running on Colab/Kaggle."
"# !pip install deeptrack # Uncomment if running on Colab/Kaggle."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "ab9551f3",
"metadata": {},
"outputs": [],
"source": [
"# !pip install optuna # Uncomment if needed."
]
},
{
Expand Down Expand Up @@ -932,7 +942,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "py_env_book",
"display_name": "deeptrack2",
"language": "python",
"name": "python3"
},
Expand All @@ -946,7 +956,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.15"
"version": "3.13.14"
}
},
"nbformat": 4,
Expand Down
15 changes: 12 additions & 3 deletions tutorials/1-getting-started/DTGS131_tracking_multiple_particles_unet.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,16 @@
"metadata": {},
"outputs": [],
"source": [
"# !pip install deeplay deeptrack # Uncomment if running on Colab/Kaggle."
"# !pip install deeptrack # Uncomment if running on Colab/Kaggle."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# !pip install deeplay # Uncomment if needed."
]
},
{
Expand Down Expand Up @@ -825,7 +834,7 @@
"provenance": []
},
"kernelspec": {
"display_name": "py_env_book (3.10.15)",
"display_name": "deeptrack2",
"language": "python",
"name": "python3"
},
Expand All @@ -839,7 +848,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.15"
"version": "3.13.14"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
Expand Down
16 changes: 13 additions & 3 deletions tutorials/1-getting-started/DTGS141_distinguishing_particles_in_brightfield.ipynb
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Expand Up @@ -15,7 +15,17 @@
"metadata": {},
"outputs": [],
"source": [
"# !pip install deeplay deeptrack # Uncomment if running on Colab/Kaggle."
"# !pip install deeptrack # Uncomment if running on Colab/Kaggle."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# !pip install deeplay # Uncomment if needed.\n",
"# !pip install seaborn # Uncomment if needed."
]
},
{
Expand Down Expand Up @@ -803,7 +813,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "deeptrack2",
"language": "python",
"name": "python3"
},
Expand All @@ -817,7 +827,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.9"
"version": "3.13.14"
}
},
"nbformat": 4,
Expand Down
18 changes: 14 additions & 4 deletions tutorials/1-getting-started/DTGS151_unsupervised_object_detection_with_lodestar.ipynb
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Expand Up @@ -12,7 +12,7 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"id": "98c6d466",
"metadata": {
"execution": {
Expand All @@ -24,7 +24,17 @@
},
"outputs": [],
"source": [
"# !pip install deeplay deeptrack # Uncomment if running on Colab/Kaggle."
"# !pip install deeptrack # Uncomment if running on Colab/Kaggle."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "33a22dbc",
"metadata": {},
"outputs": [],
"source": [
"# !pip install deeplay # Uncomment if needed."
]
},
{
Expand Down Expand Up @@ -607,7 +617,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "py_env_book (3.10.15)",
"display_name": "deeptrack2",
"language": "python",
"name": "python3"
},
Expand All @@ -621,7 +631,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.15"
"version": "3.13.14"
}
},
"nbformat": 4,
Expand Down
15 changes: 12 additions & 3 deletions tutorials/1-getting-started/DTGS161_torch_fitting.ipynb
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Expand Up @@ -11,13 +11,22 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# !pip install deeptrack # Uncomment if running on Colab/Kaggle."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# !pip install torch # Uncomment if needed."
]
},
{
"cell_type": "markdown",
"metadata": {},
Expand Down Expand Up @@ -500,7 +509,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "py_env_book (3.10.15)",
"display_name": "deeptrack2",
"language": "python",
"name": "python3"
},
Expand All @@ -514,7 +523,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.15"
"version": "3.13.14"
}
},
"nbformat": 4,
Expand Down
4 changes: 2 additions & 2 deletions tutorials/1-getting-started/DTGS172_bacteria.ipynb
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Expand Up @@ -741,7 +741,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "py_env_book (3.10.15)",
"display_name": "deeptrack2",
"language": "python",
"name": "python3"
},
Expand All @@ -755,7 +755,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.15"
"version": "3.13.14"
}
},
"nbformat": 4,
Expand Down
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