diff --git a/.github/workflows/lint-and-dryrun-testing.yml b/.github/workflows/lint-and-dryrun-testing.yml
index c10af65..d113d67 100644
--- a/.github/workflows/lint-and-dryrun-testing.yml
+++ b/.github/workflows/lint-and-dryrun-testing.yml
@@ -10,40 +10,42 @@ jobs:
     name: Lint code
     runs-on: ubuntu-latest
     steps:
+      - name: Clone repo
+        uses: actions/checkout@v4
+
       - name: Install non-python dependencies
         run: |
           sudo apt-get install -y graphviz-dev
+
       - name: Setup Python environment
-        uses: khanlab/actions/.github/actions/action-setup_task-installPyProject@v0.3.6
+        uses: prefix-dev/setup-pixi@v0.8.14
         with:
-          python-version: '3.10'
-      - name: yamlfix
-        run: poetry run poe yamlfix-check
-      - name: ruff
-        run: poetry run poe ruff-lint-check
+          environments: >-
+            dev-only
+          activate-environment: dev-only
+
+      - name: isort
+        run: isort autoafids/*.py -c
+
+      - name: black
+        run: black autoafids --check
+
       - name: snakefmt
-        run: poetry run poe snakefmt-check
+        run: snakefmt autoafids --check
+
   test:
     runs-on: ubuntu-latest
     needs: [quality]
-    defaults:
-      run:
-        shell: bash -l {0}
+
     steps:
       - name: checkout repository
         uses: actions/checkout@v4
-      - name: Setup Miniforge and mamba
-        uses: conda-incubator/setup-miniconda@v3
+
+      - name: Setup Pixi environment
+        uses: prefix-dev/setup-pixi@v0.8.14
         with:
-          miniforge-variant: Miniforge3
-          miniforge-version: latest
-          mamba-version: '*'
-          use-mamba: true
-          conda-solver: libmamba
-          auto-activate-base: true
-      - name: Install snakebids
-        run: |
-          mamba install snakebids -c bioconda -c conda-forge -y
+          activate-environment: true
+
       - name: Setup env for autoafids
         run: |
           echo "AUTOAFIDS_CACHE_DIR=`pwd`/test_data/autoafids_cache_dir" >> $GITHUB_ENV
diff --git a/.github/workflows/push_conda.yml b/.github/workflows/push_conda.yml
index e0a964e..fb7d617 100644
--- a/.github/workflows/push_conda.yml
+++ b/.github/workflows/push_conda.yml
@@ -74,4 +74,4 @@ jobs:
             --user khanlab \
             --label main \
             --force \
-            "$PACKAGE_PATH"
+            "$PACKAGE_PATH"
\ No newline at end of file
diff --git a/.github/workflows/wetrun-testing.yml b/.github/workflows/wetrun-testing.yml
index fcf5df8..50488e4 100644
--- a/.github/workflows/wetrun-testing.yml
+++ b/.github/workflows/wetrun-testing.yml
@@ -15,25 +15,10 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
-      - name: Setup Miniforge and mamba
-        uses: conda-incubator/setup-miniconda@v3
+      - name: Setup Pixi environment
+        uses: prefix-dev/setup-pixi@v0.8.14
         with:
-          miniforge-variant: Miniforge3
-          miniforge-version: latest
-          mamba-version: '*'
-          use-mamba: true
-          conda-solver: libmamba
-          auto-activate-base: true
-      - name: Create environment with snakebids
-        run: |
-          mamba create -n snakebids-env snakebids scikit-learn pandas -c bioconda -c conda-forge -y
-      - name: Cache Snakemake Conda environments
-        uses: actions/cache@v4
-        with:
-          path: test_data/autoafids_cache_dir/conda
-          key: conda-env-${{ hashFiles('autoafids/workflow/envs/*.yaml') }}
-          restore-keys: |
-            conda-env-
+          activate-environment: true
       - name: Restore cached CNN model
         uses: actions/cache@v4
         with:
@@ -45,19 +30,16 @@ jobs:
       - name: Run wet-run test for T1w modality
         shell: bash -l {0}
         run: |
-          conda activate snakebids-env
           ./autoafids/run.py test_data/bids_wetrun_testing/bids_T1w test_out participant \
             --cores all --force-output --stereotaxy STN --fidqc --conda-frontend mamba | tee autoafids_output.log
       - name: Model accuracy check
         shell: bash -l {0}
         run: |
-          conda activate snakebids-env
           python ./tests/test_fcsv_output.py \
             --autoafids_fcsv ./test_out/sub-001/afids-cnn/*.fcsv \
             --baseline_fcsv ./test_data/bids_wetrun_testing/bids_T1w/sub-001/anat/sub-001*.fcsv | tee test_fcsv_output.log
       - name: Run wet-run test for T2w modality
         shell: bash -l {0}
         run: |-
-          conda activate snakebids-env
           ./autoafids/run.py test_data/bids_wetrun_testing/bids_T2w test_out participant \
             --modality T2w --cores all --force-output --conda-frontend mamba
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 8fa269d..8a4fdfe 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -17,7 +17,7 @@ formats: [pdf]
 build:
   os: ubuntu-20.04
   tools:
-    python: '3.10'
+    python: '3.11'
 python:
   install:
     - requirements: docs/requirements.txt
diff --git a/autoafids-dev.yml b/autoafids-dev.yml
deleted file mode 100644
index ba145a6..0000000
--- a/autoafids-dev.yml
+++ /dev/null
@@ -1,14 +0,0 @@
----
-name: autoafids-dev
-channels: [conda-forge, bioconda, defaults]
-dependencies:
-  - python=3.10
-  - snakebids=0.14.0
-  - black >=23.7.0,<24.0.0
-  - isort >=5.12.0,<6.0.0
-  - poethepoet>=0.10.0,<0.11.0
-  - ruff >=0.0.282,<0.0.283
-  - snakefmt >=0.8.4,<0.9.0
-  - yamlfix >=1.11.0,<2.0.0
-  - pygraphviz ==1.7
-  - jinja2 >=3.0.3,<4.0.0
diff --git a/autoafids/run.py b/autoafids/run.py
index 4f7b033..5558be2 100755
--- a/autoafids/run.py
+++ b/autoafids/run.py
@@ -5,9 +5,7 @@
 from snakebids import bidsapp, plugins
 
 try:
-    from autoafids.workflow.lib import (
-        utils as utils,  # Works when run as a package
-    )
+    from autoafids.workflow.lib import utils as utils  # Works when run as a package
 except ImportError:
     from workflow.lib import utils as utils  # Works when run directly
 
@@ -30,6 +28,7 @@
 if "SNAKEMAKE_CONDA_PREFIX" not in os.environ:
     os.environ["SNAKEMAKE_CONDA_PREFIX"] = str(conda_prefix)
 
+
 def get_parser():
     """Exposes parser for sphinx doc generation, cwd is the docs dir"""
     return app.build_parser().parser
diff --git a/autoafids/workflow/Snakefile b/autoafids/workflow/Snakefile
index fc357a3..bee657d 100644
--- a/autoafids/workflow/Snakefile
+++ b/autoafids/workflow/Snakefile
@@ -129,7 +129,7 @@ if config["modality"] != "T1w":
             bids(
                 root="logs",
                 suffix="synthsr_output.txt",
-                **inputs[config["modality"]].wildcards
+                **inputs[config["modality"]].wildcards,
             ),
         resources:
             mem_mb=10000,
@@ -147,19 +147,21 @@ if "n4_bias_correction" in profile_settings and config["modality"] == "T1w":
 
     rule n4_bias_correction:
         input:
-            im=bids(
-                root=str(Path(config["bids_dir"])),
-                datatype="anat",
-                suffix="T1w.nii.gz",
-                **inputs[config["modality"]].wildcards,
-            )
-            if config["modality"] == "T1w"
-            else bids(
-                root=work,
-                datatype="SynthSR",
-                desc=f"{config['modality']}-SynthSR",
-                suffix="T1w.nii.gz",
-                **inputs[config["modality"]].wildcards,
+            im=(
+                bids(
+                    root=str(Path(config["bids_dir"])),
+                    datatype="anat",
+                    suffix="T1w.nii.gz",
+                    **inputs[config["modality"]].wildcards,
+                )
+                if config["modality"] == "T1w"
+                else bids(
+                    root=work,
+                    datatype="SynthSR",
+                    desc=f"{config['modality']}-SynthSR",
+                    suffix="T1w.nii.gz",
+                    **inputs[config["modality"]].wildcards,
+                )
             ),
         output:
             corrected_im=bids(
@@ -167,7 +169,7 @@ if "n4_bias_correction" in profile_settings and config["modality"] == "T1w":
                 datatype="n4biascorr",
                 desc="n4corrected",
                 suffix="T1w.nii.gz",
-                **inputs[config["modality"]].wildcards
+                **inputs[config["modality"]].wildcards,
             ),
         conda:
             "envs/ants.yaml"
@@ -177,36 +179,42 @@ if "n4_bias_correction" in profile_settings and config["modality"] == "T1w":
 
 rule norm_im:
     input:
-        im_raw=lambda wildcards: bids(
-            root=work,
-            datatype="synthstrip",
-            desc="synthstrip",
-            suffix="T1w.nii.gz",
-            **inputs[config["modality"]].wildcards,
-        )
-        if "skull_strip" in profile_settings
-        else bids(
-            root=work,
-            datatype="n4biascorr",
-            desc="n4corrected",
-            suffix="T1w.nii.gz",
-            **inputs[config["modality"]].wildcards,
-        )
-        if "n4_bias_correction" in profile_settings
-        and config["modality"] == "T1w"
-        else bids(
-            root=str(Path(config["bids_dir"])),
-            datatype="anat",
-            suffix="T1w.nii.gz",
-            **inputs[config["modality"]].wildcards,
-        )
-        if config["modality"] == "T1w"
-        else bids(
-            root=work,
-            datatype="SynthSR",
-            desc=f"{config['modality']}-SynthSR",
-            suffix="T1w.nii.gz",
-            **inputs[config["modality"]].wildcards,
+        im_raw=lambda wildcards: (
+            bids(
+                root=work,
+                datatype="synthstrip",
+                desc="synthstrip",
+                suffix="T1w.nii.gz",
+                **inputs[config["modality"]].wildcards,
+            )
+            if "skull_strip" in profile_settings
+            else (
+                bids(
+                    root=work,
+                    datatype="n4biascorr",
+                    desc="n4corrected",
+                    suffix="T1w.nii.gz",
+                    **inputs[config["modality"]].wildcards,
+                )
+                if "n4_bias_correction" in profile_settings
+                and config["modality"] == "T1w"
+                else (
+                    bids(
+                        root=str(Path(config["bids_dir"])),
+                        datatype="anat",
+                        suffix="T1w.nii.gz",
+                        **inputs[config["modality"]].wildcards,
+                    )
+                    if config["modality"] == "T1w"
+                    else bids(
+                        root=work,
+                        datatype="SynthSR",
+                        desc=f"{config['modality']}-SynthSR",
+                        suffix="T1w.nii.gz",
+                        **inputs[config["modality"]].wildcards,
+                    )
+                )
+            )
         ),
     output:
         im_norm=bids(
@@ -254,28 +262,32 @@ if "resample_im" in profile_settings and config["modality"] == "T1w":
 
 rule regmni2sub:
     input:
-        im_resamp=bids(
-            root=work,
-            datatype="n4biascorr",
-            desc="n4corrected",
-            suffix="T1w.nii.gz",
-            **inputs[config["modality"]].wildcards,
-        )
-        if "n4_bias_correction" in profile_settings
-        and config["modality"] == "T1w"
-        else bids(
-            root=str(Path(config["bids_dir"])),
-            datatype="anat",
-            suffix="T1w.nii.gz",
-            **inputs[config["modality"]].wildcards,
-        )
-        if config["modality"] == "T1w"
-        else bids(
-            root=work,
-            datatype="SynthSR",
-            desc=f"{config['modality']}-SynthSR",
-            suffix="T1w.nii.gz",
-            **inputs[config["modality"]].wildcards,
+        im_resamp=(
+            bids(
+                root=work,
+                datatype="n4biascorr",
+                desc="n4corrected",
+                suffix="T1w.nii.gz",
+                **inputs[config["modality"]].wildcards,
+            )
+            if "n4_bias_correction" in profile_settings
+            and config["modality"] == "T1w"
+            else (
+                bids(
+                    root=str(Path(config["bids_dir"])),
+                    datatype="anat",
+                    suffix="T1w.nii.gz",
+                    **inputs[config["modality"]].wildcards,
+                )
+                if config["modality"] == "T1w"
+                else bids(
+                    root=work,
+                    datatype="SynthSR",
+                    desc=f"{config['modality']}-SynthSR",
+                    suffix="T1w.nii.gz",
+                    **inputs[config["modality"]].wildcards,
+                )
+            )
         ),
     output:
         xfm_slicer=bids(
@@ -351,29 +363,33 @@ rule all:
                 datatype="afids-cnn",
                 desc="afidscnn",
                 suffix="afids.fcsv",
-                **inputs[config["modality"]].wildcards
+                **inputs[config["modality"]].wildcards,
             ),
         ),
-        fidqc=inputs[config["modality"]].expand(
-            bids(
-                root=root,
-                datatype="fidqc",
-                desc="fidqc",
-                suffix="afids.html",
-                **inputs[config["modality"]].wildcards
+        fidqc=(
+            inputs[config["modality"]].expand(
+                bids(
+                    root=root,
+                    datatype="fidqc",
+                    desc="fidqc",
+                    suffix="afids.html",
+                    **inputs[config["modality"]].wildcards,
+                )
             )
-        )
-        if config["fidqc"]
-        else [],
-        afidspred=inputs[config["modality"]].expand(
-            bids(
-                root=root,
-                datatype="stereotaxy",
-                desc=stereotaxy_target,
-                suffix="native.fcsv",
-                **inputs[config["modality"]].wildcards
+            if config["fidqc"]
+            else []
+        ),
+        afidspred=(
+            inputs[config["modality"]].expand(
+                bids(
+                    root=root,
+                    datatype="stereotaxy",
+                    desc=stereotaxy_target,
+                    suffix="native.fcsv",
+                    **inputs[config["modality"]].wildcards,
+                )
             )
-        )
-        if config["stereotaxy"]
-        else [],
+            if config["stereotaxy"]
+            else []
+        ),
     default_target: True
diff --git a/autoafids/workflow/rules/cnn.smk b/autoafids/workflow/rules/cnn.smk
index cc096c3..3404054 100644
--- a/autoafids/workflow/rules/cnn.smk
+++ b/autoafids/workflow/rules/cnn.smk
@@ -25,7 +25,7 @@ rule applyfidmodel:
                 datatype="normalize",
                 desc=chosen_norm_method,
                 suffix="T1w.nii.gz",
-                **inputs[config["modality"]].wildcards
+                **inputs[config["modality"]].wildcards,
             )
             if config["modality"] != "T1w"
             else bids(
@@ -34,7 +34,7 @@ rule applyfidmodel:
                 desc=chosen_norm_method,
                 res=config["res"],
                 suffix="T1w.nii.gz",
-                **inputs[config["modality"]].wildcards
+                **inputs[config["modality"]].wildcards,
             )
         ),
         prior=bids(
@@ -52,13 +52,13 @@ rule applyfidmodel:
             datatype="afids-cnn",
             desc="afidscnn",
             suffix="afids.fcsv",
-            **inputs[config["modality"]].wildcards
+            **inputs[config["modality"]].wildcards,
         ),
     log:
         bids(
             root="logs",
             suffix="landmark.log",
-            **inputs[config["modality"]].wildcards
+            **inputs[config["modality"]].wildcards,
         ),
     conda:
         "../envs/tensorflow.yaml"
diff --git a/autoafids/workflow/rules/fidqc.smk b/autoafids/workflow/rules/fidqc.smk
index e0f5190..820a98e 100644
--- a/autoafids/workflow/rules/fidqc.smk
+++ b/autoafids/workflow/rules/fidqc.smk
@@ -5,7 +5,7 @@ rule fidqc:
             datatype="afids-cnn",
             desc="afidscnn",
             suffix="afids.fcsv",
-            **inputs[config["modality"]].wildcards
+            **inputs[config["modality"]].wildcards,
         ),
         im=bids(
             root=str(Path(config["bids_dir"])),
@@ -19,7 +19,7 @@ rule fidqc:
             datatype="fidqc",
             desc="fidqc",
             suffix="afids.html",
-            **inputs[config["modality"]].wildcards
+            **inputs[config["modality"]].wildcards,
         ),
     params:
         refim=str(Path(workflow.basedir).parent / config["templatet1w"]),
diff --git a/autoafids/workflow/rules/stereotaxy.smk b/autoafids/workflow/rules/stereotaxy.smk
index f439c97..cb79382 100644
--- a/autoafids/workflow/rules/stereotaxy.smk
+++ b/autoafids/workflow/rules/stereotaxy.smk
@@ -8,7 +8,7 @@ rule stereotaxy:
             datatype="afids-cnn",
             desc="afidscnn",
             suffix="afids.fcsv",
-            **inputs[config["modality"]].wildcards
+            **inputs[config["modality"]].wildcards,
         ),
     output:
         fcsv_native=bids(
@@ -16,21 +16,21 @@ rule stereotaxy:
             datatype="stereotaxy",
             desc=stereotaxy_target,
             suffix="native.fcsv",
-            **inputs[config["modality"]].wildcards
+            **inputs[config["modality"]].wildcards,
         ),
         fcsv_mcp=bids(
             root=root,
             datatype="stereotaxy",
             desc=stereotaxy_target,
             suffix="mcp.fcsv",
-            **inputs[config["modality"]].wildcards
+            **inputs[config["modality"]].wildcards,
         ),
         ACPC_txt=bids(
             root=work,
             datatype="ACPCtransforms",
             desc="transform",
             suffix="ACPC.txt",
-            **inputs[config["modality"]].wildcards
+            **inputs[config["modality"]].wildcards,
         ),
     params:
         model=str(Path(workflow.basedir).parent / config[stereotaxy_target]),
diff --git a/autoafids/workflow/scripts/apply.py b/autoafids/workflow/scripts/apply.py
index 15af6b1..e1d27e4 100644
--- a/autoafids/workflow/scripts/apply.py
+++ b/autoafids/workflow/scripts/apply.py
@@ -19,10 +19,11 @@
 
 tf.autograph.set_verbosity(0)  # Turn off epoch progress.
 
-from numpy.typing import NDArray
-from typing import Union
-from pathlib import Path
 import csv
+from pathlib import Path
+from typing import Union
+
+from numpy.typing import NDArray
 
 AFIDS_FIELDNAMES = [
     "id",
@@ -85,9 +86,7 @@ def afids_to_fcsv(
         row["z"] = afid_coords[label][2]
 
     # Write output fcsv
-    with Path(fcsv_output).open(
-        "w", encoding="utf-8", newline=""
-        ) as out_fcsv_file:
+    with Path(fcsv_output).open("w", encoding="utf-8", newline="") as out_fcsv_file:
         for line in header:
             out_fcsv_file.write(line)
         writer = csv.DictWriter(out_fcsv_file, fieldnames=AFIDS_FIELDNAMES)
@@ -95,7 +94,6 @@ def afids_to_fcsv(
             writer.writerow(row)
 
 
-
 def load_fcsv(fcsv_path: Union[PathLike[str], str]) -> pd.DataFrame:
     """
     Loads fcsv.
@@ -187,10 +185,7 @@ def fid_world2voxel(
     return fid_voxel.astype(int)
 
 
-def gen_patch_slices(
-        centre: NDArray,
-        radius: int
-        ) -> tuple[slice, slice, slice]:
+def gen_patch_slices(centre: NDArray, radius: int) -> tuple[slice, slice, slice]:
     """
     Generate patch slices
 
@@ -206,10 +201,7 @@ def gen_patch_slices(
     -------
         Image patches around center coordinate
     """
-    return tuple(
-        slice(coord - radius, coord + radius + 1
-              ) for coord in centre[:3]
-        )
+    return tuple(slice(coord - radius, coord + radius + 1) for coord in centre[:3])
 
 
 def slice_img(img: NDArray, centre: NDArray, radius: int) -> NDArray:
diff --git a/autoafids/workflow/scripts/norm_schemes.py b/autoafids/workflow/scripts/norm_schemes.py
index ef40ed8..b5a9cba 100644
--- a/autoafids/workflow/scripts/norm_schemes.py
+++ b/autoafids/workflow/scripts/norm_schemes.py
@@ -35,12 +35,7 @@ def normalize(method, input_im, output_im):
     elif method == "zscore":
         nii_data_normalized = (nii_data - nii_data.mean()) / (nii_data.std())
 
-    nib.save(
-        nib.Nifti1Image(
-            nii_data_normalized,
-            affine=nii_affine), output_im
-            )
-
+    nib.save(nib.Nifti1Image(nii_data_normalized, affine=nii_affine), output_im)
 
 
 normalize(
diff --git a/autoafids/workflow/scripts/qc.py b/autoafids/workflow/scripts/qc.py
index 7a4e5c2..bc73be5 100644
--- a/autoafids/workflow/scripts/qc.py
+++ b/autoafids/workflow/scripts/qc.py
@@ -97,8 +97,7 @@ def generate_html_with_keypress(
 
     for label, images in subject_images.items():
         num_slices = len(images)
-        has_reference = ( reference_images is not None
-                         and label in reference_images )
+        has_reference = reference_images is not None and label in reference_images
 
         html_content += f"""
         <div class="container">
@@ -119,10 +118,7 @@ def generate_html_with_keypress(
     """
 
     for label, images in subject_images.items():
-        has_reference = (
-            reference_images is not None
-            and label in reference_images
-              )
+        has_reference = reference_images is not None and label in reference_images
         html_content += f"""
             subjects["{label}"] = {{
                 targetImages: {images},
@@ -169,19 +165,12 @@ def generate_html_with_keypress(
         f.write(html_content)
 
 
-def save_single_slice_in_memory(
-        data, x, y, z,
-        offset,
-        zoom_radius,
-        show_crosshairs
-    ):
+def save_single_slice_in_memory(data, x, y, z, offset, zoom_radius, show_crosshairs):
     fig, axes = plt.subplots(1, 3, figsize=(15, 5))
 
     for i, (slice_data, coord, title) in enumerate(
         zip(
-            [data[x + offset, :, :],
-            data[:, y + offset, :],
-            data[:, :, z + offset]],
+            [data[x + offset, :, :], data[:, y + offset, :], data[:, :, z + offset]],
             [(y, z), (x, z), (x, y)],
             ["Sagittal", "Coronal", "Axial"],
         )
@@ -203,11 +192,7 @@ def save_single_slice_in_memory(
     return base64.b64encode(buffer.read()).decode()
 
 
-def save_mri_slices_as_images(
-        data, x, y, z,
-        jitter,
-        zoom_radius,
-        show_crosshairs=True):
+def save_mri_slices_as_images(data, x, y, z, jitter, zoom_radius, show_crosshairs=True):
     return Parallel(n_jobs=-1)(
         delayed(save_single_slice_in_memory)(
             data, x, y, z, offset, zoom_radius, show_crosshairs
@@ -216,7 +201,6 @@ def save_mri_slices_as_images(
     )
 
 
-
 def extract_coordinates_from_fcsv(file_path, label_description):
     df = pd.read_csv(file_path, comment="#", header=None)
     row = df[df[11] == label_description]
diff --git a/autoafids/workflow/scripts/run_synthsr.py b/autoafids/workflow/scripts/run_synthsr.py
index c202e7d..845e834 100644
--- a/autoafids/workflow/scripts/run_synthsr.py
+++ b/autoafids/workflow/scripts/run_synthsr.py
@@ -4,12 +4,7 @@
 
 
 # run SynthSR
-def run_program(
-        input_img,
-        output_img,
-        modality,
-        log_file
-    ):
+def run_program(input_img, output_img, modality, log_file):
 
     cmd = [
         "python",
@@ -17,7 +12,7 @@ def run_program(
         "SynthSR.scripts.predict_command_line",
         input_img,
         output_img,
-        "--cpu"
+        "--cpu",
     ]
 
     if modality == "ct":
@@ -25,12 +20,7 @@ def run_program(
 
     with open(log_file, "a") as log:
         try:
-            subprocess.run(
-                cmd,
-                check=True,
-                stdout=log,
-                stderr=log
-            )
+            subprocess.run(cmd, check=True, stdout=log, stderr=log)
             logging.info(
                 f"SynthSR processing completed for {input_img}."
                 f"Output saved to {output_img}"
@@ -40,15 +30,12 @@ def run_program(
             raise
 
 
-log_file=snakemake.log[0]
-download_dir=snakemake.params["download_dir"]
+log_file = snakemake.log[0]
+download_dir = snakemake.params["download_dir"]
 
 run_program(
     input_img=snakemake.input["im"],
     output_img=snakemake.output["SynthSR"],
     modality=snakemake.params["modality"],
-    log_file=log_file
+    log_file=log_file,
 )
-
-
-
diff --git a/autoafids/workflow/scripts/stereotaxy.py b/autoafids/workflow/scripts/stereotaxy.py
index 315e433..24d5c64 100644
--- a/autoafids/workflow/scripts/stereotaxy.py
+++ b/autoafids/workflow/scripts/stereotaxy.py
@@ -204,12 +204,14 @@ def fids_to_fcsv(fids, fcsv_template, fcsv_output):
     with open(fcsv_output, "w") as f:
         f.write("\n".join(line for line in fcsv))
 
+
 def make_zero(num, threshold=0.0001):
     if abs(num) < threshold:
         return 0
     else:
         return num
 
+
 def mcp_origin(df_afids):
     """
     sets MCP as the origin point for each of the subjects
@@ -241,6 +243,7 @@ def mcp_origin(df_afids):
         np.array([mcp_x.to_numpy(), mcp_y.to_numpy(), mcp_z.to_numpy()])
     )
 
+
 def get_fiducial_index(fid):
     """
     Retrieve the index corresponding to the fiducial name or integer.
@@ -278,7 +281,7 @@ def fcsvtodf(fcsv_path):
     try:
         subject_id = re.search(r"(sub-\w+)", fcsv_path).group(1)
     except Exception as e:
-       print("no subject id found")
+        print("no subject id found")
 
     # Read in .fcsv file, skip header
     df_raw = pd.read_table(fcsv_path, sep=",", header=2)
@@ -304,6 +307,7 @@ def fcsvtodf(fcsv_path):
 
     return df_xyz_clean, df_raw.shape[0]
 
+
 def compute_distance(fcsv_path, fid1, fid2):
     """
     Compute the Euclidean distance between two fiducials.
@@ -335,6 +339,7 @@ def compute_distance(fcsv_path, fid1, fid2):
 
     return xyz_diff.flatten(), distance
 
+
 def compute_average(fcsv_path, fid1, fid2):
     """
     Compute the average position between two fiducials.
@@ -400,11 +405,7 @@ def generate_slicer_file(matrix, filename):
 
 
 def acpcmatrix(
-    fcsv_path,
-    midline,
-    center_on_mcp=False,
-    write_matrix=True,
-    transform_file_name=None
+    fcsv_path, midline, center_on_mcp=False, write_matrix=True, transform_file_name=None
 ):
     """
     Computes a 4x4 transformation matrix aligning with the AC-PC axis.
@@ -509,12 +510,12 @@ def transform_afids(fcsv_path, slicer_tfm, midpoint):
         fcsv_df.loc[:, "z"] = tcoords[:, 2]
     else:
         raise ValueError(
-            "New coordinates do not match " +
-            "the number of rows in the original fcsv."
+            "New coordinates do not match " + "the number of rows in the original fcsv."
         )
 
     return fcsv_df, xfm_txt
 
+
 def model_pred(
     in_fcsv: str,
     model: str,
@@ -584,12 +585,10 @@ def model_pred(
     num_cols = df_sub_mcp.select_dtypes(include="number")
     cols_to_modify = (num_cols > -0.0001).all() & (num_cols < 0.0001).all()
 
-    df_sub_mcp.loc[:, cols_to_modify] = (
-        df_sub_mcp.loc[:, cols_to_modify]
-        .applymap(make_zero)
+    df_sub_mcp.loc[:, cols_to_modify] = df_sub_mcp.loc[:, cols_to_modify].applymap(
+        make_zero
     )
 
-
     # Load the trained model components from the pickle file
     with open(model, "rb") as file:
         objects_dict = pickle.load(file)
@@ -604,11 +603,7 @@ def model_pred(
     df_sub_mcp = pca.transform(df_sub_mcp)
 
     # Make predictions using Ridge regression models for x, y, z coordinates
-    y_sub = np.column_stack(
-        [
-            ridge.predict(df_sub_mcp) for ridge in ridge_inference
-        ]
-        )
+    y_sub = np.column_stack([ridge.predict(df_sub_mcp) for ridge in ridge_inference])
 
     # Adjust the second predicted x-coordinate to reflect the left hemisphere
     y_sub[1, 0] *= -1
diff --git a/pixi.lock b/pixi.lock
new file mode 100644
index 0000000..deff238
--- /dev/null
+++ b/pixi.lock
@@ -0,0 +1,7673 @@
+version: 6
+environments:
+  default:
+    channels:
+    - url: https://conda.anaconda.org/conda-forge/
+    - url: https://conda.anaconda.org/bioconda/
+    indexes:
+    - https://pypi.org/simple
+    packages:
+      linux-64:
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/acres-0.5.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/aiohappyeyeballs-2.6.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aiohttp-3.13.2-py313h321d83c_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/aiosignal-1.4.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.14-hb9d3cd8_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/amply-0.1.6-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aom-3.9.1-hac33072_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/appdirs-1.4.4-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/archspec-0.2.5-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/argparse-dataclass-2.0.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/arrow-1.4.0-pyhcf101f3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/astor-0.8.1-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.2-h39aace5_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-25.4.0-pyh71513ae_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/bcrypt-5.0.0-py313h843e2db_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/bids-validator-1.14.7.post0-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/bidsschematools-1.1.2-pyhd8ed1ab_0.conda
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+      - conda: https://conda.anaconda.org/conda-forge/linux-64/dbus-1.13.6-h5008d03_3.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/distro-1.9.0-pyhd8ed1ab_1.conda
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-    {file = "wrapt-1.17.2-py3-none-any.whl", hash = "sha256:b18f2d1533a71f069c7f82d524a52599053d4c7166e9dd374ae2136b7f40f7c8"},
-    {file = "wrapt-1.17.2.tar.gz", hash = "sha256:41388e9d4d1522446fe79d3213196bd9e3b301a336965b9e27ca2788ebd122f3"},
-]
-
-[[package]]
-name = "yamlfix"
-version = "1.16.0"
-description = "A simple opionated yaml formatter that keeps your comments!"
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "yamlfix-1.16.0-py3-none-any.whl", hash = "sha256:d92bf8a6d5b6f186bd9d643d633549a1c2424555cb8d176a5d38bce3e678b2b0"},
-    {file = "yamlfix-1.16.0.tar.gz", hash = "sha256:72f7990e5b2b4459ef3249df4724dacbd85ce7b87f4ea3503d8a72c48574cc32"},
-]
-
-[package.dependencies]
-click = ">=8.1.3"
-maison = ">=1.4.0"
-ruyaml = ">=0.91.0"
-
-[[package]]
-name = "yte"
-version = "1.8.1"
-description = "A YAML template engine with Python expressions"
-optional = false
-python-versions = "<4.0,>=3.7"
-files = [
-    {file = "yte-1.8.1-py3-none-any.whl", hash = "sha256:4fa0ddfff047984bda0bc521d85cba32a8a7ca4c4cdb16938b6911c049485733"},
-    {file = "yte-1.8.1.tar.gz", hash = "sha256:6eefbdceae56e156ba9881ecb63f3c9217cfe5d5cc6f85fdb061c266a8eff112"},
-]
-
-[package.dependencies]
-dpath = ">=2.1,<3.0"
-plac = ">=1.3.4,<2.0"
-pyyaml = ">=6.0,<7.0"
-
-[[package]]
-name = "zipp"
-version = "3.23.0"
-description = "Backport of pathlib-compatible object wrapper for zip files"
-optional = false
-python-versions = ">=3.9"
-files = [
-    {file = "zipp-3.23.0-py3-none-any.whl", hash = "sha256:071652d6115ed432f5ce1d34c336c0adfd6a884660d1e9712a256d3d3bd4b14e"},
-    {file = "zipp-3.23.0.tar.gz", hash = "sha256:a07157588a12518c9d4034df3fbbee09c814741a33ff63c05fa29d26a2404166"},
-]
-
-[package.extras]
-check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
-cover = ["pytest-cov"]
-doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-enabler = ["pytest-enabler (>=2.2)"]
-test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more_itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
-type = ["pytest-mypy"]
-
-[metadata]
-lock-version = "2.0"
-python-versions = ">=3.9,<4.0"
-content-hash = "0e260bc56576fa1834a3da9ce8ac0d28d87238aa459802b1567f5bcc5e6e0bef"
diff --git a/pyproject.toml b/pyproject.toml
index 2be7d05..7ac0e45 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,72 +1,56 @@
-[tool.poetry]
+[project]
 name = "autoafids"
 version = "1.1.0"
 description = "End-to-end SnakeBIDS workflow for landmark regression and derivative apps"
 readme = "README.md"
 license = "MIT"
-authors = [
-    "Alaa Taha <ataha24@uwo.ca>"
-]
-classifiers = [
-    "Programming Language :: Python :: 3",
-    "Operating System :: OS Independent",
-]
+authors = [{name = "Alaa Taha", email = "ataha24@uwo.ca"}]
+requires-python = ">= 3.11"
+dependencies = []
+scripts = { autoafids = "autoafids.run:app.run" }
 
-[tool.poetry.dependencies]
-python = ">=3.9,<4.0"
-snakebids = "0.14.0"
-appdirs = "^1.4.4"
-pulp = { version="<2.8.0", python = "<3.11" }
-pyvista = "^0.44.2"
+[build-system]
+build-backend = "hatchling.build"
+requires = ["hatchling"]
 
-[tool.poetry.group.dev.dependencies]
-black = "^23.7.0"
-isort = "^5.12.0"
-poethepoet = "^0.21.1"
-ruff = "^0.0.282"
-snakefmt = "^0.8.4"
-yamlfix = "^1.11.0"
-pygraphviz = "1.7"
-Jinja2 = "^3.0.3"
+[tool.pixi.workspace]
+channels = ["conda-forge", "bioconda"]
+platforms = ["linux-64"]
 
-[tool.poetry.scripts]
-autoafids = "autoafids.run:app.run"
+[tool.pixi.feature.runtime.dependencies]
+snakebids = ">=0.14.0,<0.15"
+appdirs = ">=1.4.4,<2.0.0"
+pyvista = ">=0.44.2,<0.45.0"
+conda = ">=25.5.0,<26"
 
+[tool.pixi.feature.dev.dependencies]
+black = ">=24.0.0,<25.0.0"
+isort = ">=5.10.1,<6.0.0"
+poethepoet = ">=0.10.0,<0.11.0"
+snakefmt = ">=0.10.0,<0.11.0"
+pygraphviz = "*"
+Jinja2 = ">=3.0.3,<4.0.0"
 
-[build-system]
-requires = ["poetry-core>=1.0.0"]
-build-backend = "poetry.core.masonry.api"
+[tool.pixi.environments.default]
+features = ["runtime"]
 
-[tool.poe.tasks]
-setup = "pre-commit install"
-ruff-lint = "ruff check --fix autoafids"
-ruff-lint-check = "ruff check autoafids"
-snakefmt = "snakefmt autoafids"
-snakefmt-check = "snakefmt --check autoafids"
-quality = ["yamlfix", "ruff-lint", "snakefmt"]
-quality-check = ["yamlfix-check", "ruff-lint-check", "snakefmt-check"]
+[tool.pixi.environments.dev]
+features = ["runtime", "dev"]
 
-[tool.poe.tasks.yamlfix]
-shell = """
-find . -type f \\( \
-    -iname \\*.yaml -o -iname \\*.yml ! -iname snakemake* \
-    ! -iname snakebids* \
-\\) -exec yamlfix {} \\;
-"""
+[tool.pixi.environments.dev-only]
+features = ["dev"]
 
-[tool.poe.tasks.yamlfix-check]
-shell = """
-find . -type f \\( \
-    -iname \\*.yaml -o -iname \\*.yml ! -iname snakemake* \
-    ! -iname snakebids* \
-\\) -exec yamlfix --check {} \\;
-"""
+[tool.pixi.pypi-dependencies]
+autoafids = { path = ".", editable = true }
 
-[tool.ruff]
-select = ["E", "W", "N", "RUF", "I", "UP"]
-line-length = 79
-builtins = ["snakemake"]
+[tool.isort]
+profile = "black"
+multi_line_output = 3
 
 [tool.snakefmt]
 line_length = 79
-include = '\.smk$|^Snakefile'
\ No newline at end of file
+include = '\.smk$|^Snakefile'
+
+[tool.pixi.tasks]
+quality_check = "isort autoafids/*.py -c && black autoafids --check && snakefmt autoafids --check"
+quality_fix = "isort autoafids/*.py && black autoafids && snakefmt autoafids"
\ No newline at end of file
diff --git a/recipe/meta.yaml b/recipe/meta.yaml
index c805abd..21bca02 100644
--- a/recipe/meta.yaml
+++ b/recipe/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "autoafids" %}
 {% set version = "1.1.0" %}
-{% set ref = "241e4b3ddecc82f1e245ad3c881b516a44ee33cd" %}
+{% set ref = "0495778fac62a789ba0970804fa007a73e18a6c9" %}
 
 package:
   name: {{ name|lower }}
@@ -8,7 +8,7 @@ package:
 
 source:
   url: https://github.com/afids/autoafids/archive/{{ ref }}.tar.gz
-  sha256: cffa7619612fc2d43b1363ccc76744d04d2c6ff8f3cb549f22a75caf2ff6d8ae
+  sha256: 1c749b2c7d38f288e6590ee682998e8d27c99979e0b02ae5830f0bd5a11ad0a6
 
 build:
   entry_points: 
@@ -19,34 +19,30 @@ build:
 
 requirements:
   host:
-    - python
-    - poetry-core
+    - python >=3.11
+    - hatchling
+    - hatch-vcs
     - pip
   run:
-    - python >=3.9,<4.0
-    - snakebids >=0.14.0
+    - python >=3.11
+    - snakebids >=0.14.0,<0.15
     - appdirs >=1.4.4,<2.0.0
-    - pulp <2.8.0  # [py<311]
     - pyvista >=0.44.2,<0.45.0
 
 test:
   imports:
-    - autoafids
+      - autoafids
   commands:
     - autoafids --help
 
 
 about:
   home: https://github.com/afids/autoafids
-  summary: |
-    End-to-end BIDS app for automated anatomical fiducial landmark regression.
-  description: |
-    AutoAFIDs is a BIDS-compliant application that automates the placement 
-    and evaluation of anatomical fiducial landmarks (AFIDs).
+  summary: End-to-end BIDS app for automated anatomical fiducial landmark regression.
+  description: AutoAFIDs is a BIDS-compliant application that automates the placement and evaluation of anatomical fiducial landmarks (AFIDs).
   license: MIT
   license_file: LICENSE
 
-
 extra:
   recipe-maintainers:
     - Dhananjhay
\ No newline at end of file